[1] "ofn"         "-oTKIPAN-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/15081103/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/15087102/transformed.cor.cli.txt"

nPatients in clinical file=914, in cluster file=882, common to both=859
[1]  82 859
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               30               829 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               30               829 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               68               791 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               68               791 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              116               743 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              116               743 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              124               735 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              124               735 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               98               761 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               98               761 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              151               708 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              151               708 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               46               813 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               46               813 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               813 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               813 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              236               623 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              236               623 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              246               613 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              246               613 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               838 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               838 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               843 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               843 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              356               503 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              356               503 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              358               501 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              358               501 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               64               795 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               64               795 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               96               763 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               96               763 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               833 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               833 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               835 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               835 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                830 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                29                830 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                837 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                837 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                57                802 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                57                802 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                55                804 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                55                804 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               245                614 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               245                614 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               249                610 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               249                610 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                51                808 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                51                808 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                820 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                820 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                807 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                807 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               270                589 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               270                589 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               258                601 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               258                601 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               187                672 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               187                672 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               210                649 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               210                649 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                805 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                805 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                50                809 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                50                809 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                75                784 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                75                784 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                781 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                781 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               224                635 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               224                635 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               228                631 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               228                631 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                73                786 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                73                786 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                797 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                62                797 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              117               742 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              117               742 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              118               741 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              118               741 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              139               720 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              139               720 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              107               752 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              107               752 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               63               796 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               63               796 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               62               797 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               62               797 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              409               450 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              409               450 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              122               737 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              122               737 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               96               763 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               96               763 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               90               769 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               90               769 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               24               835 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               24               835 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               22               837 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               22               837 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              170               689 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              170               689 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              204               655 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              204               655 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               855 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               855 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               855 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               855 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               698 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               698 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               85               774 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               85               774 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              191               668 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              191               668 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              193               666 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              193               666 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               129                730 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               129                730 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               154                705 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               154                705 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                818 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                41                818 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                808 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                808 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                853 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                853 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                855 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                855 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               136                723 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               136                723 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               260                599 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               260                599 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                67                792 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                67                792 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                18                841 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                18                841 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                831 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                831 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               105                754 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               105                754 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                80                779 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                80                779 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               139                720 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               139                720 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                713 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                713 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                26                833 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                26                833 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                837 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                837 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                847 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                847 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                853 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                853 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               130                729 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               130                729 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               104                755 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               104                755 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              115               744 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              115               744 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              113               746 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              113               746 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 859 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=198,	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=589,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "858"  
freq.contrast "858"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=42,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=44,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 859 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "RACE"                          "ETHNICITY"                    
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
462 123 251  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
462 123 251  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
462 123 251  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
462 123 251  15 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
317  43   6 
[1] "table(vv)"
vv
 N0  N1  N2 
317  43   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
317  43   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
317  43   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=42, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=39, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED    12  17
  1P GAIN WILD-TYPE 620 194
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               29               814 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               17               194 
$`1P GAIN MUTATED`
TCGA-KN-8428 TCGA-A3-3372 TCGA-AK-3430 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-4838 
       52.27        24.16        15.78        22.45        52.21        27.42 
TCGA-B0-5092 TCGA-B0-5109 TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4352 TCGA-BP-4756 
       15.09        19.30        23.31         0.53        11.31        12.30 
TCGA-BP-4771 TCGA-BP-4974 TCGA-BP-5175 TCGA-CJ-4873 TCGA-CJ-5679 TCGA-CJ-6027 
        5.33         7.23        30.64        74.27        22.32        60.99 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-5452 TCGA-MM-A564 TCGA-AL-A5DJ 
       83.90        18.77        69.21        58.82        19.96        49.25 
TCGA-BQ-5893 TCGA-G7-6789 TCGA-GL-7966 TCGA-IA-A40Y TCGA-WN-A9G9 
        7.92         4.01         3.68         2.04        26.01 

$`1P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       84.36        73.08        66.31        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        45.93        28.73        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       29.95        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        0.53         4.64         5.46         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       12.33        33.99        31.33        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        49.38        45.50        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       48.10         6.35        79.30         1.78        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 
       66.31        78.18        74.66         1.35       105.93       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45        46.16         0.59        47.08        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       63.42         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       57.21        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC 
       70.13        35.87         2.01        19.43        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       44.61         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95        11.97         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.53              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            83.90            194.79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            22.32             30.89 
[1] "0.5 - 83.9 (22.3)"  "0.1 - 194.8 (30.9)"
[1] "hr=" "3.3"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         7        4        12        7
  1P GAIN WILD-TYPE     441       99       178       93
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 7               441
  STAGE II                4                99
  STAGE III              12               178
  STAGE IV                7                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     8   4  18   0
  1P GAIN WILD-TYPE 454 119 233  15
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               8               454
  T2               4               119
  T3              18               233
  T4               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"
                   vv
clus                 N0  N1  N2
  1P GAIN MUTATED    11   5   1
  1P GAIN WILD-TYPE 306  38   5
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              11               306
  N1               5                38
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    17   6
  1P GAIN WILD-TYPE 525  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     17    6
  1P GAIN WILD-TYPE  525   83
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              17               525
  1               6                83
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    13  17
  1P GAIN WILD-TYPE 274 555
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     13   17
  1P GAIN WILD-TYPE  274  555
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              13               274
  MALE                17               555
[1] 2 2
[1] FALSE
D1V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1P GAIN MUTATED                    1                                22
  1P GAIN WILD-TYPE                 65                               502
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1P GAIN MUTATED                                       7
  1P GAIN WILD-TYPE                                   262
D1V9, multiclass
                                       clus
vv                                      1P GAIN MUTATED 1P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  22               502
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                89 
       TCGA-KL-8324        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-KO-8409        TCGA-KO-8416        TCGA-A3-A8CQ        TCGA-A3-A8OV 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-A8OW        TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-5164        TCGA-B8-A54E        TCGA-B8-A54F        TCGA-B8-A54G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B8-A8YJ        TCGA-DV-A4W0        TCGA-G6-A5PC        TCGA-G6-A8L7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JD        TCGA-2Z-A9JI        TCGA-2Z-A9JK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JQ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-8310        TCGA-A4-A48D 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4115        TCGA-B9-4117 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-7268        TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GL-A59T        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HE-A5NK        TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"1P GAIN WILD-TYPE" 
D1V11, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                1                66 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-B2-A4SR        TCGA-B8-5158 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A563        TCGA-MM-A84U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-UZ-A9PX        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           2    26
  1P GAIN WILD-TYPE                       114   676
D1V12, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      2               114
  WHITE                                         26               676
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  22
  1P GAIN WILD-TYPE  42 575
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   22
  1P GAIN WILD-TYPE   42  575
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO              22               575
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    37  30
  1Q GAIN WILD-TYPE 595 181
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               67               776 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               30               181 
$`1Q GAIN MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
       49.08        34.29        31.07        24.16        18.87        15.78 
TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4838 TCGA-B0-4848 
       58.49        22.45         6.64        52.21        27.42        29.03 
TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5109 TCGA-B0-5115 TCGA-B0-5701 TCGA-B4-5843 
       15.09         2.24        19.30        26.20        56.94         0.36 
TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 
       23.31         0.53        90.28        61.78        64.27        80.68 
TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4974 
       74.17        11.31        12.30         5.33        68.38         7.23 
TCGA-BP-5173 TCGA-BP-5175 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 
        1.78        30.64        46.55        65.69        74.27        64.27 
TCGA-CJ-4881 TCGA-CJ-4916 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 
       66.21        45.14        18.81        79.89        18.87        22.32 
TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 
       60.99        73.18        83.90        18.77        46.16        69.21 
TCGA-CZ-5452 TCGA-G6-A5PC TCGA-MM-A564 TCGA-2Z-A9J2 TCGA-A4-7287 TCGA-A4-A5Y1 
       58.82         7.96        19.96        59.01        19.63        12.99 
TCGA-AL-3466 TCGA-AL-A5DJ TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
        9.63        49.25        30.28        25.35         7.66         0.95 
TCGA-BQ-5893 TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-Q2-A5QZ 
        7.92         4.01        16.90         3.68         2.04        14.07 
TCGA-WN-A9G9 
       26.01 

$`1Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       86.10        77.85        57.17        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       24.69        37.38        48.82        21.86         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       60.92        72.07        68.61        67.20        57.37        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        42.08        40.01        48.69        45.93        28.73 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 
        5.98         2.14        19.73         3.16        43.96         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       20.25        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       45.30        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       65.29        39.45        26.07         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        10.95         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       84.92        90.12        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        14.27        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       16.27        14.17       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       77.03        62.24        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 
       71.80        48.07        13.15        61.68        10.82        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       60.59        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 
       63.25        73.22        14.17        75.88        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       47.18        75.06        77.36        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4918 
       49.18        49.28        50.33        54.48        38.56         3.06 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 
        4.57        63.88        72.00        84.66        25.71        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
       74.66         1.35       105.93       103.43        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        61.41        63.42         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       15.25        10.85         7.04        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 
       22.49         0.13        12.82        11.57        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        8.48        16.31        15.75         8.28        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        2.10        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
       43.20        47.80        21.63        40.83        26.04        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25        10.88        11.97         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        17.75        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        27.39        12.99        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.36              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            90.28            194.79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           25.350            30.905 
[1] "0.4 - 90.3 (25.4)"  "0.1 - 194.8 (30.9)"
[1] "hr=" "2.2"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED        20        9        28       11
  1Q GAIN WILD-TYPE     428       94       162       89
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                20               428
  STAGE II                9                94
  STAGE III              28               162
  STAGE IV               11                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q GAIN MUTATED    23  11  34   0
  1Q GAIN WILD-TYPE 439 112 217  15
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              23               439
  T2              11               112
  T3              34               217
  T4               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"
                   vv
clus                 N0  N1  N2
  1Q GAIN MUTATED    28   9   1
  1Q GAIN WILD-TYPE 289  34   5
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              28               289
  N1               9                34
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    46  11
  1Q GAIN WILD-TYPE 496  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     46   11
  1Q GAIN WILD-TYPE  496   78
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              46               496
  1              11                78
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    25  43
  1Q GAIN WILD-TYPE 262 529
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     25   43
  1Q GAIN WILD-TYPE  262  529
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              25               262
  MALE                43               529
[1] 2 2
[1] FALSE
D2V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1Q GAIN MUTATED                    0                                51
  1Q GAIN WILD-TYPE                 66                               473
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1Q GAIN MUTATED                                      17
  1Q GAIN WILD-TYPE                                   252
D2V9, multiclass
                                       clus
vv                                      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  51               473
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              17               252
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     1
  1Q GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           5    61
  1Q GAIN WILD-TYPE                       111   641
D2V12, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      5               111
  WHITE                                         61               641
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     3  48
  1Q GAIN WILD-TYPE  39 549
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      3   48
  1Q GAIN WILD-TYPE   39  549
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              48               549
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    88  28
  2P GAIN WILD-TYPE 544 183
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              116               727 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               28               183 
$`2P GAIN MUTATED`
TCGA-KN-8427 TCGA-KO-8410 TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ 
        0.99        87.78        12.66        24.16        18.87         0.10 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3444 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 
       66.31        15.78        48.36         1.41        19.73         3.16 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-5099 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5702 
       46.59         0.59        15.95        19.30        11.80        52.77 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5549 
        0.23         5.46         0.36        25.55        23.74         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 
       14.27         0.53         4.93       101.06         0.43        61.78 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4347 TCGA-BP-4351 
        0.07        93.99        18.48        74.17        44.94        31.89 
TCGA-BP-4756 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4799 
       12.30        41.75        13.15        60.59        68.38        37.25 
TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5173 TCGA-BP-5178 
       47.97        58.98        31.30         3.88         1.78        62.86 
TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4876 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
       37.22        34.95        64.27        24.66        59.44        47.67 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5682 
       51.29        49.28        63.88        72.00        84.66        61.91 
TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 
       53.42        83.77        73.18        66.31        74.66        46.16 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
       69.21        58.75         6.77        56.28        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 TCGA-2Z-A9J5 TCGA-A4-A4ZT 
       10.85        31.10        67.96         3.91       100.27        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU 
        8.48        16.31        15.75         9.63        13.55         2.20 
TCGA-B1-7332 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5893 
        7.33        10.16         0.46         2.10        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 
        2.76        96.92        13.61        51.19         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF 
       51.78        39.25        17.33         3.68        17.95        68.12 
TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        16.80         2.04        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V 
       34.29        42.94        84.95        17.75        14.07        28.80 
TCGA-SX-A7SQ TCGA-UZ-A9PK 
       41.62        60.03 

$`2P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67        80.38       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW 
       20.28        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 
      109.91        29.10        84.36        73.08        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 
       68.61        67.20        57.37        46.78        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        3.32         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 
       43.96         6.64         3.25        20.25        15.72         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        52.08        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        29.95        35.90 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         0.53         4.64         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       27.16        27.55        25.05        24.66        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       17.16        16.60        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
       14.17       111.02        85.51        94.72        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 
       62.07        80.68        37.25        21.21        15.16        52.24 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       62.86        54.77        49.08        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       33.99        31.33        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       44.15        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       61.97        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       60.30        61.22        61.51         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
       27.22        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
       79.30        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        44.55        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 
       27.65        39.45        50.24        56.35        49.97        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
        4.57        18.81        79.89        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       25.25        18.15        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       60.99        75.58        62.66         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
       81.83         5.39        85.78        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        25.45         0.59        47.08 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 
       63.42        58.82         0.82        23.74        18.44        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       55.33        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40         1.94        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.02        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 
       10.85         7.04        75.55        59.01        58.22        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 
        0.76        19.63        19.73        14.33        12.46         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 
       12.99        12.46        58.45        76.64        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61        49.25        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
       20.61         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25        10.88         7.66         0.95       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       13.08         2.40         0.43        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       25.15        13.68        25.84         6.38        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
        0.89        11.21         4.60        13.41        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
        5.49        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 
       21.34        16.34        12.36         0.13        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        99.78        87.22         6.61        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        12.85        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       33.04        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        18.02        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           101.06            194.79 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            24.41             30.64 
[1] "0.1 - 101.1 (24.4)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        56       12        32       15
  2P GAIN WILD-TYPE     392       91       158       85
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                56               392
  STAGE II               12                91
  STAGE III              32               158
  STAGE IV               15                85
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P GAIN MUTATED    57  15  40   4
  2P GAIN WILD-TYPE 405 108 211  11
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              57               405
  T2              15               108
  T3              40               211
  T4               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"
                   vv
clus                 N0  N1  N2
  2P GAIN MUTATED    41  11   1
  2P GAIN WILD-TYPE 276  32   5
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              41               276
  N1              11                32
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    75  13
  2P GAIN WILD-TYPE 467  76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     75   13
  2P GAIN WILD-TYPE  467   76
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              75               467
  1              13                76
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    38  78
  2P GAIN WILD-TYPE 249 494
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     38   78
  2P GAIN WILD-TYPE  249  494
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              38               249
  MALE                78               494
[1] 2 2
[1] FALSE
D3V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2P GAIN MUTATED                    2                                74
  2P GAIN WILD-TYPE                 64                               450
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2P GAIN MUTATED                                      40
  2P GAIN WILD-TYPE                                   229
D3V9, multiclass
                                       clus
vv                                      2P GAIN MUTATED 2P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  2                64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  74               450
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              40               229
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, continuous
D3V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     2
  2P GAIN WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          11   100
  2P GAIN WILD-TYPE                       105   602
D3V12, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                     11               105
  WHITE                                        100               602
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     6  78
  2P GAIN WILD-TYPE  36 519
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6   78
  2P GAIN WILD-TYPE   36  519
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              78               519
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    94  30
  2Q GAIN WILD-TYPE 538 181
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              124               719 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               30               181 
$`2Q GAIN MUTATED`
TCGA-KN-8427 TCGA-KO-8410 TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ 
        0.99        87.78        12.66        24.16        18.87         0.10 
TCGA-AK-3429 TCGA-AK-3444 TCGA-AK-3450 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 
       66.31        48.36        58.49         1.41        19.73         3.16 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-5099 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5702 
       46.59         0.59        15.95        19.30        11.80        52.77 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5549 
        0.23         5.46         0.36        25.55        23.74         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4170 
       14.27         0.53         4.93       101.06         0.43        77.03 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4347 
       61.78         0.07        93.99        18.48        74.17        44.94 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 
       31.89        12.30        41.75        13.15        60.59        68.38 
TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5001 
       37.25        47.97        58.98        31.30         3.88        38.70 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4644 
        1.78        74.20        62.86        37.22        34.95        11.05 
TCGA-CJ-4876 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 
       64.27        24.66        59.44        47.67        51.29        49.28 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6032 
       63.88        72.00        84.66        61.91        53.42        83.77 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4859 
       73.18        66.31        74.66        46.16        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 
        6.77        56.28        55.33        47.01        10.85        31.10 
TCGA-EU-5905 TCGA-2Z-A9J5 TCGA-2Z-A9JR TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
        3.91       100.27         5.29        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 
       15.75         9.63        13.55        44.61         2.20         7.33 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5893 
        6.58        10.16         0.46         2.10        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 
        2.76        96.92        13.61        51.19         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T 
       51.78        39.25        25.84        17.33         3.68        17.95 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE 
       68.12        11.84        16.80         2.04        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       11.41        34.29        42.94        84.95        17.75        14.07 
TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ 
       28.80        41.62        60.03        86.27 

$`2Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67        80.38       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW 
       20.28        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
      109.91        29.10        84.36        73.08        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3445 
       72.07        68.61        67.20        57.37        46.78        42.08 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        3.32         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 
       43.96         6.64         3.25        20.25        15.72         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        52.08        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        29.95        35.90 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         0.53         4.64         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       27.16        27.55        25.05        24.66        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       17.16        16.60        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
       14.17       111.02        85.51        94.72        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
       32.61        99.85        89.36        23.05        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 
       80.68        37.25        21.21        15.16        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       54.77        49.08        12.23        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       31.33        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        10.98        36.95         6.71 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 
       36.23        28.87        48.10         6.35        79.30        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27         9.63        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97        58.92        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 
       45.14         3.06         4.57        18.81        79.89        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        25.25        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       67.00        53.26        60.99        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5589 
       64.57        92.02        81.83         5.39        85.78        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
        0.59        47.08        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       18.44        56.94        55.33        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       66.28        56.84        23.90        66.02        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        15.25        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       59.01        58.22        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       12.46         8.28        12.99        12.46        58.45        76.64 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       30.35        25.08        49.25        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       16.87         3.55        16.77         0.46        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
       20.61         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       13.25        10.88         7.66         0.95       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
       13.08         2.40         0.43        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92        27.65         1.05        12.43         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       11.21         4.60        13.41        56.75        73.25         5.49 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       16.34        12.36         0.13        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       99.78        87.22         6.61        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        12.85        47.90        47.44        33.04 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR 
       27.06        11.93        19.00        38.63        16.31        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        18.02        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           101.06            194.79 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           25.695            30.640 
[1] "0.1 - 101.1 (25.7)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        62       12        32       17
  2Q GAIN WILD-TYPE     386       91       158       83
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                62               386
  STAGE II               12                91
  STAGE III              32               158
  STAGE IV               17                83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q GAIN MUTATED    63  16  41   4
  2Q GAIN WILD-TYPE 399 107 210  11
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              63               399
  T2              16               107
  T3              41               210
  T4               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"
                   vv
clus                 N0  N1  N2
  2Q GAIN MUTATED    44  11   2
  2Q GAIN WILD-TYPE 273  32   4
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              44               273
  N1              11                32
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    79  14
  2Q GAIN WILD-TYPE 463  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     79   14
  2Q GAIN WILD-TYPE  463   75
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              79               463
  1              14                75
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    44  80
  2Q GAIN WILD-TYPE 243 492
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     44   80
  2Q GAIN WILD-TYPE  243  492
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              44               243
  MALE                80               492
[1] 2 2
[1] FALSE
D4V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2Q GAIN MUTATED                    2                                77
  2Q GAIN WILD-TYPE                 64                               447
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2Q GAIN MUTATED                                      45
  2Q GAIN WILD-TYPE                                   224
D4V9, multiclass
                                       clus
vv                                      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  2                64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  77               447
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              45               224
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     2
  2Q GAIN WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          12   107
  2Q GAIN WILD-TYPE                       104   595
D4V12, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                     12               104
  WHITE                                        107               595
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V13, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     7  85
  2Q GAIN WILD-TYPE  35 512
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7   85
  2Q GAIN WILD-TYPE   35  512
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO              85               512
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    72  19
  3P GAIN WILD-TYPE 560 192
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               91               752 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               192 
$`3P GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 
       98.96        28.11        24.79        62.37        49.97         0.99 
TCGA-KN-8428 TCGA-A3-3374 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4712 
       52.27        43.20        57.37        45.93         3.62        43.96 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B4-5835 TCGA-BP-4337 TCGA-BP-4352 TCGA-BP-4969 
       11.90         7.30         0.53         0.07        11.31        58.98 
TCGA-BP-4994 TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4897 TCGA-CW-6087 
       43.00        30.64        19.82        14.17        59.44         1.35 
TCGA-CZ-5456 TCGA-CZ-5469 TCGA-2K-A9WE TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-A4-7287 
       56.28        31.10         7.04       100.27        56.91        19.63 
TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.97         0.76        19.73        14.33        12.46        16.96 
TCGA-A4-A5DU TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 
       16.31        76.64        13.55         2.20         7.33         6.58 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       30.58        10.16        28.18         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-7045 
       43.99        22.06        17.49        47.80        26.04        48.26 
TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 
       96.92         7.04         3.81        11.61        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 
       24.46        40.77        51.19        13.08         2.40        51.78 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF 
       17.98        16.90       194.79        17.95        11.21        68.12 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84         5.49        85.78        11.97        29.10        11.41 
TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVM TCGA-PJ-A5Z9 TCGA-SX-A71V TCGA-SX-A7SN 
       87.22         6.61        50.60        17.75        28.80        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-UZ-A9PV 
       16.31        41.62        48.30        60.03        52.11        25.68 
TCGA-Y8-A895 
       15.91 

$`3P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61        67.20        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        3.16         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       20.94        43.30        11.24        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       21.21        15.16        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       63.25        73.22        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
       73.18        66.31        78.18        74.66       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        15.25        10.85        75.55        59.01        58.22 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
        0.13        12.82        11.57        18.21        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-A57E 
       29.46        25.64        23.28        23.31        19.63         8.48 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M 
       30.35        25.08        44.61        49.25        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       24.56        16.87         3.55        16.77         0.46        33.83 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 
       10.09        34.49        12.46        50.50        26.40        20.61 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
        2.10        19.23         6.81         0.16        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5561 
       26.27        20.12        11.28         7.63         7.17        13.61 
TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
      129.86        13.78         3.75        14.63         3.02        79.86 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       10.68         1.18         0.43         4.01        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       17.33        80.65        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
       12.43         0.89         4.60        13.41        56.75        73.25 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99         2.04        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55W TCGA-MH-A55Z 
       21.34        16.34        12.36         0.13        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       21.44        15.48        99.78        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        78.90        12.85        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR 
       47.44        33.04        27.06        11.93        38.63        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       38.86        30.67        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       18.64        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.07              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           194.79            151.96 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            22.06             31.30 
[1] "0.1 - 194.8 (22.1)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1"  
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        57       14        11       11
  3P GAIN WILD-TYPE     391       89       179       89
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                57               391
  STAGE II               14                89
  STAGE III              11               179
  STAGE IV               11                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P GAIN MUTATED    58  17  18   3
  3P GAIN WILD-TYPE 404 106 233  12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              58               404
  T2              17               106
  T3              18               233
  T4               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"
                   vv
clus                 N0  N1  N2
  3P GAIN MUTATED    21   8   1
  3P GAIN WILD-TYPE 296  35   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              21               296
  N1               8                35
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    42   7
  3P GAIN WILD-TYPE 500  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     42    7
  3P GAIN WILD-TYPE  500   82
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              42               500
  1               7                82
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27  71
  3P GAIN WILD-TYPE 260 501
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   71
  3P GAIN WILD-TYPE  260  501
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              27               260
  MALE                71               501
[1] 2 2
[1] FALSE
D5V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3P GAIN MUTATED                    8                                19
  3P GAIN WILD-TYPE                 58                               505
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3P GAIN MUTATED                                      71
  3P GAIN WILD-TYPE                                   198
D5V9, multiclass
                                       clus
vv                                      3P GAIN MUTATED 3P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                  19               505
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              71               198
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, continuous
D5V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     2
  3P GAIN WILD-TYPE                                1    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          13    76
  3P GAIN WILD-TYPE                       103   626
D5V12, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                     13               103
  WHITE                                         76               626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  74
  3P GAIN WILD-TYPE  38 523
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   74
  3P GAIN WILD-TYPE   38  523
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                38
  NOT HISPANIC OR LATINO              74               523
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   108  36
  3Q GAIN WILD-TYPE 524 175
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              144               699 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               36               175 
$`3Q GAIN MUTATED`
TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 
       98.96        28.11        24.79        62.37        49.97         0.99 
TCGA-KN-8428 TCGA-A3-3325 TCGA-A3-3374 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3453 
       52.27        24.69        43.20        68.61        57.37        45.93 
TCGA-B0-4690 TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4833 TCGA-B0-4845 
        1.41         3.62        43.96         6.64        78.44        65.29 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5097 TCGA-B0-5109 TCGA-B0-5116 TCGA-B0-5696 
       11.90         7.30        21.86        19.30        21.60        56.78 
TCGA-B0-5710 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4620 TCGA-B8-4621 
       47.97         0.53         5.46        23.31        25.55        25.91 
TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4337 TCGA-BP-4338 
        6.38         0.53        93.34        89.36         0.07        93.99 
TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4960 TCGA-BP-4969 TCGA-BP-4985 
       11.31         5.98        44.15        71.41        58.98        31.30 
TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4640 
       43.00         6.35        30.64        19.82        14.17        65.69 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-6028 TCGA-CJ-6033 TCGA-CW-5591 TCGA-CW-6087 
       59.44        47.67        53.42         7.36        74.66         1.35 
TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 
       18.77        69.21         6.77        56.28        47.01        57.21 
TCGA-CZ-5465 TCGA-CZ-5469 TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       47.54        31.10         7.04        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
       56.91        19.63        30.48        23.97        23.31         0.76 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        16.31        15.75 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-4103 
       76.64        13.55         2.20         7.33         6.58        30.58 
TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.16        28.18         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 
       22.06         2.10        17.49        47.80        26.04         7.66 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 
       48.26        96.92         7.04         3.81        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       24.46        40.77        80.88        51.19        54.90        34.19 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 
       13.08         2.40        51.78        17.98        16.90       194.79 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S 
       17.95        11.21        68.12        11.84         5.49        85.78 
TCGA-IA-A83W TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5E7 
       67.17        11.97        29.10        11.41        99.78        87.22 
TCGA-P4-A5EA TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V 
        6.61        16.01        50.60        17.75        14.07        28.80 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM 
       19.00        16.31        41.62        48.30        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-Y8-A895 
       21.93        52.11        30.67        25.68        12.99        15.91 

$`3Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        72.07        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        19.73         3.16         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       20.94        43.30        11.24        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        29.95        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
      101.13        15.78        46.68        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        1.25         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 
       27.55        25.05        24.66        17.19        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       16.60        14.27        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        32.61        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       15.16        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4763 
       31.33        12.30        72.59        77.98        77.62        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10        79.30         1.78        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22        75.88        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       62.10        73.35        67.00        53.26        60.99        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       62.66        83.77        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 
       85.78        73.18        66.31        78.18       105.93        83.90 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 
      103.43        25.45        46.16         0.59        47.08        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5466 
       56.94        55.33        10.85        10.22        21.76        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       19.96        15.25        10.85        75.55         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       11.57        18.21        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 
        0.89         0.23        16.64        29.46        25.64        23.28 
TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       19.63         8.48         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
       58.45        30.35        25.08        44.61        49.25        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       33.83        10.09        34.49        12.46        50.50        26.40 
TCGA-B9-4116 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       20.61        19.23         6.81         0.16        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 
       20.12        11.28         7.63         7.17        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 
      129.86        13.78         3.75        14.63         3.02        79.86 
TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       61.02        19.00        24.89        10.68         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 
       13.68        25.84         6.38        17.33        80.65        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE 
        3.68        27.65         1.05        12.43         0.89         4.60 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       13.41        56.75        73.25        16.80        19.99         2.04 
TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       88.24        22.26        21.34        16.34        12.36         0.13 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB 
       12.13        25.97        21.44        15.48        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S 
       92.58        52.27        78.90        12.85        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU 
       33.04        27.06        11.93        38.63        26.47        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-WN-A9G9 
       18.02         0.53        86.27        38.86        27.39        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           194.79            151.96 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            25.17             31.33 
[1] "0.1 - 194.8 (25.2)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.1"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        75       19        31       20
  3Q GAIN WILD-TYPE     373       84       159       80
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                75               373
  STAGE II               19                84
  STAGE III              31               159
  STAGE IV               20                80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q GAIN MUTATED    77  22  44   5
  3Q GAIN WILD-TYPE 385 101 207  10
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              77               385
  T2              22               101
  T3              44               207
  T4               5                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  3Q GAIN MUTATED    43  12   1
  3Q GAIN WILD-TYPE 274  31   5
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              43               274
  N1              12                31
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    72  16
  3Q GAIN WILD-TYPE 470  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     72   16
  3Q GAIN WILD-TYPE  470   73
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              72               470
  1              16                73
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    39 112
  3Q GAIN WILD-TYPE 248 460
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     39  112
  3Q GAIN WILD-TYPE  248  460
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              39               248
  MALE               112               460
[1] 2 2
[1] FALSE
D6V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3Q GAIN MUTATED                    8                                55
  3Q GAIN WILD-TYPE                 58                               469
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3Q GAIN MUTATED                                      88
  3Q GAIN WILD-TYPE                                   181
D6V9, multiclass
                                       clus
vv                                      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                  55               469
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              88               181
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, continuous
D6V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  2     2
  3Q GAIN WILD-TYPE                                0    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          18   120
  3Q GAIN WILD-TYPE                        98   582
D6V12, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                     18                98
  WHITE                                        120               582
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V13, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     7 109
  3Q GAIN WILD-TYPE  35 488
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      7  109
  3Q GAIN WILD-TYPE   35  488
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO             109               488
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    33  11
  4P GAIN WILD-TYPE 599 200
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               44               799 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               200 
$`4P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
      151.96        49.97        23.47        25.48        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 
        3.55         2.50        42.35        10.68        74.93        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3374 TCGA-AK-3430 
       87.78        86.10        77.85        57.17        43.20        15.78 
TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4813 TCGA-BP-4166 
       72.07        57.37         3.32        28.47         0.59         0.43 
TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 TCGA-AL-3466 
       74.17        11.31        14.93         3.88        43.00         9.63 
TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A8LC 
       28.18         0.16        11.97         4.01        39.25        17.33 
TCGA-SX-A7SR TCGA-WN-AB4C 
       26.47        29.00 

$`4P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
       31.33       129.37        87.91        65.19         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       87.12        19.33        11.21        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 
       76.90        79.04        92.71        16.67       103.27        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       39.16        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       60.92        68.61        67.20        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       10.68        13.08         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        26.01        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.16              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           151.96            194.79 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           28.325            30.640 
[1] "0.2 - 152.0 (28.3)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.1"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED        18       13         6        8
  4P GAIN WILD-TYPE     430       90       184       92
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                18               430
  STAGE II               13                90
  STAGE III               6               184
  STAGE IV                8                92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED    18  14  12   2
  4P GAIN WILD-TYPE 444 109 239  13
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              18               444
  T2              14               109
  T3              12               239
  T4               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4P GAIN MUTATED    26   3   2
  4P GAIN WILD-TYPE 291  40   4
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              26               291
  N1               3                40
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    24   5
  4P GAIN WILD-TYPE 518  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24    5
  4P GAIN WILD-TYPE  518   84
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              24               518
  1               5                84
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    14  32
  4P GAIN WILD-TYPE 273 540
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     14   32
  4P GAIN WILD-TYPE  273  540
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              14               273
  MALE                32               540
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4P GAIN MUTATED                   23                                13
  4P GAIN WILD-TYPE                 43                               511
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4P GAIN MUTATED                                      10
  4P GAIN WILD-TYPE                                   259
D7V9, multiclass
                                       clus
vv                                      4P GAIN MUTATED 4P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 23                43
  KIDNEY CLEAR CELL RENAL CARCINOMA                  13               511
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              10               259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     1
  4P GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           3    42
  4P GAIN WILD-TYPE                       113   660
D7V12, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      3               113
  WHITE                                         42               660
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V13, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  29
  4P GAIN WILD-TYPE  39 568
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   29
  4P GAIN WILD-TYPE   39  568
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              29               568
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    35   9
  4Q GAIN WILD-TYPE 597 202
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               44               799 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               202 
$`4Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 
      151.96        49.97        23.47        25.48        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55         2.50        11.21        42.35        10.68        74.93 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3374 
       80.38        87.78        86.10        77.85        57.17        43.20 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4696 TCGA-B0-4813 TCGA-BP-4166 
       15.78        72.07        57.37        28.47         0.59         0.43 
TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5177 
       74.17        11.31        14.93         3.88        43.00         9.63 
TCGA-B9-4114 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A8LC 
       28.18         0.16        11.97         4.01        39.25        17.33 
TCGA-SX-A7SR TCGA-WN-AB4C 
       26.47        29.00 

$`4Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 
       31.33       129.37        87.91        65.19         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       87.12        19.33        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        16.67       103.27        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        12.16        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
      109.91        29.10        84.36        73.08        66.31        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61        67.20        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        3.32         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 
        1.78        74.20        30.64        52.27        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       47.01        10.85        10.22        21.76        57.21        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       10.68        13.08         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        11.05        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 
       25.68        27.39        12.99        26.01        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.16              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           151.96            194.79 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           28.325            30.640 
[1] "0.2 - 152.0 (28.3)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.4"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q GAIN MUTATED        19       13         7        6
  4Q GAIN WILD-TYPE     429       90       183       94
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                19               429
  STAGE II               13                90
  STAGE III               7               183
  STAGE IV                6                94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED    19  14  12   1
  4Q GAIN WILD-TYPE 443 109 239  14
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              19               443
  T2              14               109
  T3              12               239
  T4               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"
                   vv
clus                 N0  N1  N2
  4Q GAIN MUTATED    25   2   2
  4Q GAIN WILD-TYPE 292  41   4
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              25               292
  N1               2                41
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    25   3
  4Q GAIN WILD-TYPE 517  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25    3
  4Q GAIN WILD-TYPE  517   86
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              25               517
  1               3                86
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16  30
  4Q GAIN WILD-TYPE 271 542
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16   30
  4Q GAIN WILD-TYPE  271  542
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              16               271
  MALE                30               542
[1] 2 2
[1] FALSE
D8V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4Q GAIN MUTATED                   24                                13
  4Q GAIN WILD-TYPE                 42                               511
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4Q GAIN MUTATED                                       9
  4Q GAIN WILD-TYPE                                   260
D8V9, multiclass
                                       clus
vv                                      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                  13               511
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               9               260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, continuous
D8V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           3    42
  4Q GAIN WILD-TYPE                       113   660
D8V12, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      3               113
  WHITE                                         42               660
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V13, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  28
  4Q GAIN WILD-TYPE  39 569
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   28
  4Q GAIN WILD-TYPE   39  569
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              28               569
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   169  65
  5P GAIN WILD-TYPE 463 146
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              234               609 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               65               146 
$`5P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 
      137.06        28.11         3.55         0.99        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 
       10.68        77.85        12.66        49.08        48.59        38.99 
TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3358 
       24.69        48.82        34.29        52.93        88.37        42.97 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-A6NL TCGA-A3-A6NN 
       24.16        43.20        18.87        65.52        22.65         0.10 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3451 
       66.31        15.78        67.20        57.37        42.08        48.69 
TCGA-AK-3453 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 
       45.93        31.27        28.04        28.47         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
       65.10         5.98        19.73         3.16        43.96         6.64 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       46.59         5.52        52.21         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
       14.93        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5094 
       29.03         2.27        20.94        43.30        18.51        10.95 
TCGA-B0-5095 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5115 
        8.05        90.87        52.54        19.30        11.80        26.20 
TCGA-B0-5121 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 
       18.21        15.78        56.78        60.33        56.94        52.77 
TCGA-B0-5705 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 TCGA-B2-5635 
      120.59        89.49        61.32        35.90        31.30        10.36 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 
        5.46        25.55        23.74        27.02         6.38        14.27 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4166 
        0.53         4.93       111.02        94.72       101.06         0.43 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 
       61.78        64.27        54.90         0.07        93.99        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       62.86        54.77        44.94        31.89        11.31        12.33 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 
        5.98        41.75        13.15        68.38        15.78        36.39 
TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 
       37.25        47.97        63.62        58.68        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4976 TCGA-BP-4983 
        6.74        57.40        58.98        48.89        53.65        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       31.30        25.81        27.22         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4999 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5168 TCGA-BP-5170 
       43.00        41.62        37.02        37.48        48.10        79.30 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5191 
        1.78        30.64         9.63        37.22        13.35        31.79 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
       34.95        31.27         0.95        46.55        63.25        75.88 
TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 
       11.05        83.97        79.66        74.27        77.36        66.21 
TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4897 TCGA-CJ-4899 
       69.86        30.64        68.55        50.01        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 
       56.35        51.29        58.92        49.28        54.48        63.88 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       79.89        84.66        22.32        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       67.00        60.99        53.42        85.78        73.18        66.31 
TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       74.66        25.45        46.16        63.39        93.04        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5462 
       63.42        58.82        56.28        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        57.21        22.52         2.40         1.94        12.69 
TCGA-CZ-5984 TCGA-CZ-5986 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5905 
       67.96        12.26        11.67        37.15        66.28         3.91 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
        4.18        10.29         2.01        19.96        10.85         7.04 
TCGA-2Z-A9J3 TCGA-4A-A93X TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D 
       58.22        12.82        30.48        29.46         0.76        12.46 
TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 
        8.48         9.63        25.08        19.56         0.46         0.46 
TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-DZ-6131 
        0.16        25.35         0.95        11.97        24.46        79.86 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK 
       19.00        13.08         4.01        17.33         1.05        73.25 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5EB TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SQ 
        2.04        11.97        84.95        16.01        14.07        41.62 

$`5P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19       104.52        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        24.16        49.02        37.15        49.58 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 
       36.36        37.38        21.86        31.07         4.50        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.63        74.76        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       28.31        20.28        15.39         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 
      109.91        29.10        84.36        73.08        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3454 
       68.61        46.78        48.36        40.01        58.49        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       22.45        37.58        38.40        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        3.32         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        7.82         2.14         3.25        20.25        15.72         0.59 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 
       45.07        33.50        16.77        54.48        29.10        68.71 
TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       45.30         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5081 
       39.45        26.07        36.85        70.52        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
        7.30        25.32        15.09         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       15.95        62.89        90.48        30.48        29.95        35.90 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 
       21.60        17.59         1.94        16.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       14.76        79.17       112.80        48.89       101.13        46.68 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       84.92        90.12        39.55        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       96.36        97.41        32.61         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       11.77        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        0.23         1.25         0.53         4.64         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 
       17.19        25.91        23.01        20.91         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       24.23        17.16        16.60        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
       16.27        14.17        85.51        90.28        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4325 
       99.85        89.36        23.05        77.03        62.24        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4349 
       21.21        15.16        18.48        52.24        49.08        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       44.15        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        20.38        10.98        36.95         6.71 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4970 TCGA-BP-4972 
        6.94        87.45        71.41        60.30        14.24        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         7.23        47.11        14.93        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       36.95         5.82        45.07        30.64        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 
       27.62        35.21        36.23        28.87         6.35        74.20 
TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.25        22.78        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4637 
       24.62        33.47        19.82        44.55        59.84        73.22 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17        65.69        54.61        53.52        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
       49.25        47.18        75.06        64.27        71.87        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4891 TCGA-CJ-4893 
       57.83        64.18        51.52        63.98        26.93        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
       27.65        39.45        47.67        49.97        49.18        50.33 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 
       38.56        45.14         3.06         4.57        18.81        72.00 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5689 TCGA-CJ-6030 
       25.71        18.87        25.25        18.15        53.26        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        5.39        78.18         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       14.66        60.59         5.46         0.82        23.74        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 
       56.94        55.33        47.01        47.54        31.10        80.19 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       65.88        12.16        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
        6.77         7.96        70.13        35.87        19.43        15.25 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       75.55        59.01       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.89         0.23        16.64        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU 
       23.31        19.63        19.73        14.33        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       15.75         8.28        12.99        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 
       13.55        30.35        44.61        49.25         2.20         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 
       21.67        24.56        16.87         3.55        16.77         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40        20.61         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         6.81        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 
       30.28        26.04        13.25        10.88         7.66         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        35.93        37.55        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92         3.68        27.65        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94         6.61        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           137.06            194.79 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           36.775            28.870 
[1] "0.1 - 137.1 (36.8)" "0.1 - 194.8 (28.9)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED       101       27        65       39
  5P GAIN WILD-TYPE     347       76       125       61
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I               101               347
  STAGE II               27                76
  STAGE III              65               125
  STAGE IV               39                61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P GAIN MUTATED   105  35  87   7
  5P GAIN WILD-TYPE 357  88 164   8
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1             105               357
  T2              35                88
  T3              87               164
  T4               7                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5P GAIN MUTATED   100  12   1
  5P GAIN WILD-TYPE 217  31   5
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             100               217
  N1              12                31
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   173  35
  5P GAIN WILD-TYPE 369  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    173   35
  5P GAIN WILD-TYPE  369   54
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             173               369
  1              35                54
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    65 171
  5P GAIN WILD-TYPE 222 401
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     65  171
  5P GAIN WILD-TYPE  222  401
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              65               222
  MALE               171               401
[1] 2 2
[1] FALSE
D9V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5P GAIN MUTATED                    8                               195
  5P GAIN WILD-TYPE                 58                               329
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5P GAIN MUTATED                                      33
  5P GAIN WILD-TYPE                                   236
D9V9, multiclass
                                       clus
vv                                      5P GAIN MUTATED 5P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                 195               329
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              33               236
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     4
  5P GAIN WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          15   212
  5P GAIN WILD-TYPE                       101   490
D9V12, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                11
  BLACK OR AFRICAN AMERICAN                     15               101
  WHITE                                        212               490
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V13, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11 157
  5P GAIN WILD-TYPE  31 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11  157
  5P GAIN WILD-TYPE   31  440
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             157               440
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   177  67
  5Q GAIN WILD-TYPE 455 144
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              244               599 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               67               144 
$`5Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8339 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 
      137.06        28.11         3.55         0.99        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 
       10.68        77.85        12.66        49.08        48.59        38.99 
TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 
       24.69        48.82        34.29        52.93        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 
       88.37        42.97        82.32        24.16        43.20        18.87 
TCGA-A3-3385 TCGA-A3-A6NL TCGA-A3-A6NN TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 
       65.52        22.65         0.10        66.31        15.78        67.20 
TCGA-AK-3440 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3460 
       57.37        48.36        42.08        48.69        45.93        31.27 
TCGA-AK-3461 TCGA-B0-4693 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 
       28.04         2.53         3.62        65.10         5.98        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 
        3.16        43.96         6.64         3.25        46.59         5.52 
TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 
       33.50         6.02        40.44        36.53        14.93        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4848 TCGA-B0-4849 
       78.44        40.70        27.42        53.88        29.03         2.27 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5102 
       20.94        43.30        18.51        10.95         8.05        90.87 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5120 
       52.54        29.95        19.30        11.80        26.20        16.21 
TCGA-B0-5121 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 
       18.21        15.78        56.78        60.33        56.94        52.77 
TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 
      120.59        47.97        89.49        61.32        35.90        31.30 
TCGA-B2-5635 TCGA-B4-5838 TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5163 
       10.36         5.46        16.80        25.55        23.74        27.02 
TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4158 
       24.23         6.38        14.27         0.53         4.93       111.02 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       94.72       101.06         0.43        61.78        64.27        54.90 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4347 
        0.07        93.99        74.17        62.86        54.77        44.94 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4768 
       31.89        11.31        12.33        44.15        41.75        13.15 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4961 
       68.38        15.78        36.39        37.25        47.97        63.62 
TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4971 TCGA-BP-4976 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4988 
       48.89        53.65        46.45        31.30        25.81        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4999 TCGA-BP-5004 TCGA-BP-5007 
       46.45        16.47        43.00        41.62        37.02        37.48 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 
       36.23        48.10        79.30         1.78        30.64         9.63 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       37.22        13.35        31.79        34.95        31.27         0.95 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 
       46.55        63.25        75.88        11.05        83.97        79.66 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 
       74.27        77.36        69.86        30.64        68.55        50.01 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 
       59.44        50.24        56.35        51.29        58.92        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
       50.33        54.48         3.06        63.88        79.89        84.66 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       22.32        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       53.42        85.78        73.18        66.31        78.18        74.66 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       25.45        46.16        63.39        93.04        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5462 
       58.82        56.28        55.33        56.94        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        57.21        22.52         2.40         1.94        12.69 
TCGA-CZ-5984 TCGA-CZ-5986 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5905 
       67.96        12.26        11.67        37.15        66.28         3.91 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
        4.18        10.29         2.01        19.96        10.85         7.04 
TCGA-4A-A93X TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E 
       12.82        30.48        29.46         0.76        12.46         8.48 
TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 
        9.63        25.08        19.56         0.46         0.46         0.16 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 
       25.35         0.95        11.97        24.46        19.00        13.08 
TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-KV-A6GD 
        4.01        17.33         1.05        73.25         2.04        11.97 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       99.78        84.95        14.07        41.62 

$`5Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19       104.52        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        24.16        49.02        37.15        49.58 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 
       36.36        37.38        21.86        31.07         4.50        45.53 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ 
       55.76        20.71        18.64        28.31        20.28        15.39 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 
       73.08        60.92        72.07        68.61        46.78        40.01 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 
       58.49        28.73        22.45        37.58        38.40        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       40.70         1.41         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4718 
       28.47        19.00         1.38         7.82         2.14        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4824 
       15.72         0.59        52.21        45.07        16.77        54.48 
TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       29.10        68.71        45.30         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 
       10.29        65.29        39.45        26.07        36.85        70.52 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5096 
       11.24        11.90         7.30        25.32        15.09         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 
       21.86        52.08        15.95        62.89        90.48        30.48 
TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5400 
       35.90        21.60        17.59         1.94        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       14.76        79.17       112.80        48.89       101.13        46.68 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 
       84.92        90.12        39.55        79.36       102.48        96.36 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       97.41        32.61         1.68        12.30        21.30        11.77 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 
       27.16        27.55        25.05        24.66        17.19        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 
       23.01        20.91         1.18         0.85        17.16        16.60 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        8.42        17.36        15.42        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       90.28        93.34        32.61        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       77.03        62.24        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       52.24        49.08        12.23        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98        77.62         5.98        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       56.91        11.64        60.95        48.95        36.53        20.38 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71         6.94        87.45        71.41 
TCGA-BP-4963 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       60.30        14.24        49.38        45.50         7.23        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4993 
       14.93        36.07        33.34        36.95         3.88         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5008 
       45.07        30.64        18.51        38.70        27.62        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 
       28.87         6.35        74.20        52.27        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 
       49.15        38.30        42.44        37.25        22.78        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       44.55        59.84        73.22        14.17        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 
       53.52        58.95        21.24        49.25        47.18        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91        57.83        64.18 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       51.52        63.98        26.93        24.66        27.65        39.45 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 
       47.67        49.97        49.18        38.56        45.14         4.57 
TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
       18.81        72.00        25.71        18.87        25.25        18.15 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.26        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       92.02        81.83         5.39         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
      103.43        18.77         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5454 
        6.77        14.66        60.59         5.46         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 
       18.44        55.33        47.01        47.54        31.10        80.19 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       65.88        12.16        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MM-A84U 
        6.77         7.96        70.13        35.87        19.43        15.25 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
       19.13         0.89         0.23        16.64        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.28        23.31        19.63        19.73        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       16.31        15.75         8.28        12.99        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       76.64        13.55        30.35        44.61        49.25         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       10.16        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.66 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       61.02        54.90        34.19        24.89        10.68         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       13.41        11.84        56.75         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36         0.13        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       21.44        15.48        87.22        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        38.63        16.31        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           137.06            194.79 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            36.46             28.80 
[1] "0.1 - 137.1 (36.5)" "0.1 - 194.8 (28.8)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED       111       27        65       40
  5Q GAIN WILD-TYPE     337       76       125       60
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I               111               337
  STAGE II               27                76
  STAGE III              65               125
  STAGE IV               40                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q GAIN MUTATED   116  35  88   6
  5Q GAIN WILD-TYPE 346  88 163   9
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1             116               346
  T2              35                88
  T3              88               163
  T4               6                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5Q GAIN MUTATED   107  12   1
  5Q GAIN WILD-TYPE 210  31   5
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0             107               210
  N1              12                31
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   183  37
  5Q GAIN WILD-TYPE 359  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    183   37
  5Q GAIN WILD-TYPE  359   52
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             183               359
  1              37                52
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    70 176
  5Q GAIN WILD-TYPE 217 396
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     70  176
  5Q GAIN WILD-TYPE  217  396
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              70               217
  MALE               176               396
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5Q GAIN MUTATED                    8                               207
  5Q GAIN WILD-TYPE                 58                               317
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5Q GAIN MUTATED                                      31
  5Q GAIN WILD-TYPE                                   238
D10V9, multiclass
                                       clus
vv                                      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                 207               317
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              31               238
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, continuous
D10V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     4
  5Q GAIN WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          16   221
  5Q GAIN WILD-TYPE                       100   481
D10V12, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                11
  BLACK OR AFRICAN AMERICAN                     16               100
  WHITE                                        221               481
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11 168
  5Q GAIN WILD-TYPE  31 429
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11  168
  5Q GAIN WILD-TYPE   31  429
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             168               429
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    13   8
  6P GAIN WILD-TYPE 619 203
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               21               822 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                8               203 
$`6P GAIN MUTATED`
TCGA-KM-8639 TCGA-KN-8427 TCGA-A3-3313 TCGA-B0-4811 TCGA-B0-5113 TCGA-B8-5549 
       31.33         0.99        24.16        46.59        11.80         6.38 
TCGA-BP-4781 TCGA-BP-4799 TCGA-BP-5177 TCGA-CJ-4885 TCGA-CZ-5460 TCGA-4A-A93X 
       68.38        37.25         9.63        69.86        47.01        12.82 
TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B9-A69E TCGA-BQ-5893 TCGA-BQ-7048 TCGA-DW-5561 
        9.63        49.25        14.86         7.92        93.34        13.61 
TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
        6.61        14.07        86.27 

$`6P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       47.21         0.53        39.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       20.25        15.72         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       54.48        29.10        10.09        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       20.38        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
       16.31        15.75         8.28        12.99        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
        2.10        19.23         6.81         0.16        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76       123.62        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17         3.81        11.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
        0.53        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.99              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            93.34            194.79 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            14.86             30.61 
[1] "1.0 - 93.3 (14.9)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "1.8"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         6        0         9        5
  6P GAIN WILD-TYPE     442      103       181       95
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 6               442
  STAGE II                0               103
  STAGE III               9               181
  STAGE IV                5                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P GAIN MUTATED     6   1  12   1
  6P GAIN WILD-TYPE 456 122 239  14
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               6               456
  T2               1               122
  T3              12               239
  T4               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"
                   vv
clus                 N0  N1  N2
  6P GAIN MUTATED     6   5   0
  6P GAIN WILD-TYPE 311  38   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               6               311
  N1               5                38
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V6, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     9   4
  6P GAIN WILD-TYPE 533  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      9    4
  6P GAIN WILD-TYPE  533   85
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0               9               533
  1               4                85
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5  16
  6P GAIN WILD-TYPE 282 556
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5   16
  6P GAIN WILD-TYPE  282  556
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5               282
  MALE                16               556
[1] 2 2
[1] FALSE
D11V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6P GAIN MUTATED                    2                                 9
  6P GAIN WILD-TYPE                 64                               515
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6P GAIN MUTATED                                      10
  6P GAIN WILD-TYPE                                   259
D11V9, multiclass
                                       clus
vv                                      6P GAIN MUTATED 6P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  2                64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   9               515
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              10               259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, continuous
D11V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           4    17
  6P GAIN WILD-TYPE                       112   685
D11V12, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                15
  BLACK OR AFRICAN AMERICAN                      4               112
  WHITE                                         17               685
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V13, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0  16
  6P GAIN WILD-TYPE  42 581
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   16
  6P GAIN WILD-TYPE   42  581
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO              16               581
[1] 2 2
[1] FALSE

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED     8   8
  6Q GAIN WILD-TYPE 624 203
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               827 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               203 
$`6Q GAIN MUTATED`
TCGA-KM-8639 TCGA-A3-3313 TCGA-B0-4811 TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 
       31.33        24.16        46.59        11.80         6.38        68.38 
TCGA-BP-4799 TCGA-CJ-4885 TCGA-4A-A93X TCGA-AL-3466 TCGA-AL-A5DJ TCGA-BQ-5893 
       37.25        69.86        12.82         9.63        49.25         7.92 
TCGA-DW-5561 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       13.61         6.61        14.07        86.27 

$`6Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        20.25        15.72         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       35.90        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        17.16        16.60        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.99        12.46        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        44.61         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95        11.97         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.17         3.81        11.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             6.38              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            86.27            194.79 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           19.115            30.580 
[1] "6.4 - 86.3 (19.1)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "2.5"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         5        0         7        3
  6Q GAIN WILD-TYPE     443      103       183       97
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 5               443
  STAGE II                0               103
  STAGE III               7               183
  STAGE IV                3                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q GAIN MUTATED     5   1   9   0
  6Q GAIN WILD-TYPE 457 122 242  15
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               5               457
  T2               1               122
  T3               9               242
  T4               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"
                   vv
clus                 N0  N1  N2
  6Q GAIN MUTATED     5   4   0
  6Q GAIN WILD-TYPE 312  39   6
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               5               312
  N1               4                39
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     7   3
  6Q GAIN WILD-TYPE 535  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      7    3
  6Q GAIN WILD-TYPE  535   86
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               7               535
  1               3                86
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     4  12
  6Q GAIN WILD-TYPE 283 560
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   12
  6Q GAIN WILD-TYPE  283  560
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4               283
  MALE                12               560
[1] 2 2
[1] FALSE
D12V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6Q GAIN MUTATED                    1                                 7
  6Q GAIN WILD-TYPE                 65                               517
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6Q GAIN MUTATED                                       8
  6Q GAIN WILD-TYPE                                   261
D12V9, multiclass
                                       clus
vv                                      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   7               517
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               8               261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, continuous
D12V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           4    12
  6Q GAIN WILD-TYPE                       112   690
D12V12, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                15
  BLACK OR AFRICAN AMERICAN                      4               112
  WHITE                                         12               690
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V13, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  13
  6Q GAIN WILD-TYPE  42 584
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   13
  6Q GAIN WILD-TYPE   42  584
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO              13               584
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   267  77
  7P GAIN WILD-TYPE 365 134
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              344               499 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               77               134 
$`7P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       62.37       151.96        49.97        23.47        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55        52.27        11.21        42.35        10.68        74.93 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 
       16.67        80.38        86.10        77.85        57.17        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3336 
       49.08        49.02        48.59        38.99        24.69        34.29 
TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 
       52.93        42.97        10.49        24.16        43.20        18.87 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3425 TCGA-AK-3427 
       65.52        20.28         0.10        11.18       109.91        84.36 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
       66.31        15.78        72.07        67.20        57.37        48.36 
TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 
       45.93         3.32         1.41         4.57         3.48        28.47 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4815 
       19.73         3.16        43.96         3.25        46.59        52.21 
TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4852 TCGA-B0-5077 
       10.09        27.42        53.88         6.71        36.85        43.30 
TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 
       10.95         2.24        90.87        19.30        11.80        21.60 
TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 TCGA-B2-3924 
       15.78        84.92        56.94        39.55        61.32        35.90 
TCGA-B2-5633 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4619 
       11.77         0.23         0.53         5.46         0.36        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I 
       25.55        25.91        23.01        14.27        29.88         4.93 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 
      111.02        85.51       101.06         0.43        89.36        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 
       62.24        61.78        64.27        97.45        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
        0.07        93.99        62.86        31.89        11.31        33.99 
TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4781 
       77.98        48.07        13.15         5.33        60.59        68.38 
TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 
       15.78        36.53        36.39        10.98        37.25         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 
       47.97        71.41        58.68        60.30         6.74        58.98 
TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       48.89        45.50        14.93        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5009 
        3.88        16.47        43.00        30.64        38.70        36.23 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5198 
        6.35        79.30         1.78         9.63        62.86        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4644 
       34.95        31.27        46.55        63.25        14.17        11.05 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 
       79.66        47.18        74.27        77.36        69.86        30.64 
TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       63.98        59.44        47.67        51.29        49.28        54.48 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 
        4.57        63.88        72.00        22.32        61.91        73.35 
TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CZ-4854 
       53.42        66.31        74.66         1.35       103.43        46.16 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5453 TCGA-CZ-5454 
       47.08        69.21         6.77        61.41         0.82        23.74 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
       56.28        55.33        47.01        10.85        57.21        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5574 
        1.94        31.10        67.96        62.63        43.69        66.28 
TCGA-G6-A8L7 TCGA-MM-A564 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       70.13        19.96         7.04        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.91         4.57        34.85        56.81        26.43        30.71 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
       12.82        61.05        19.13         0.89        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       25.64        23.97        23.31         0.76        19.63        14.33 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 
       16.96         8.48        16.31        15.75        12.46        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M 
       13.55        30.35        44.61        49.25         2.20        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
       24.56         3.55         0.46         6.58        33.83        30.58 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH 
        1.15        15.12        43.99        22.06        19.23        17.49 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5894 
       47.80        26.04        25.35        10.88         0.95         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
      123.62        48.26        96.92        50.40         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
       80.88        51.19        61.02        34.19        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 
        2.40         1.18         4.01        51.78        39.25        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 
        6.38        17.98        17.33        80.65       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH 
       27.65        12.43        17.95        11.21        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8196 
       11.84        56.75         5.49         2.04        88.24        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL 
       27.78        20.25        15.48        87.22        52.27        16.01 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PR TCGA-UZ-A9PU 
       43.76        60.03        14.83        21.93        38.86        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
       25.68        27.39        12.99        15.91        18.64        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$`7P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       86.56        66.54        73.91        28.80        54.74        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 
      129.37        87.91        25.48        65.19         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        87.78       103.27        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        12.16        36.82        47.21         0.53        39.16 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       37.15        49.58        36.36        37.38        48.82        21.86 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       82.32        51.25        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NJ TCGA-A3-A6NL 
       55.76        20.71        18.64        28.31        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 
        0.10        10.62        29.10        73.08        60.92        68.61 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        42.08        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
       40.70         1.41         2.53        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4718 
       65.10         7.82         5.98         2.14         6.64        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 
       78.44        68.71        40.70        45.30        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       70.52        20.94        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       18.51        15.09         8.05        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        29.95        35.90 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 
       46.68        56.78        60.33        90.12        52.77       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 
       79.36       102.48        47.97        96.36        89.49        97.41 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
       32.61         1.68        12.30        21.30        31.30        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         5.75         1.25 
TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.05        24.66        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 
        0.85        24.23        17.16        16.60         6.38         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       34.39        14.30        27.29        17.06         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4161 
       17.36        15.42        16.27        14.17        94.72        90.28 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 
       93.34        32.61        99.85        23.05        54.90        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4340 
        3.58        27.78        62.07        80.68        21.21        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        74.17        54.77        49.08        44.94        12.23 
TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 
       12.33        31.33        12.30        72.59        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 
       44.15        41.75        71.80        61.68        10.82        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
       13.51        56.91        11.64        60.95        48.95        20.38 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 
       36.95         6.94        87.45        63.62        61.22        61.51 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       57.40        14.24        49.38         7.23        47.11        53.65 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 
       36.07        33.34        25.81        27.22        46.45         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       45.07        41.62        18.51        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       35.21        28.87        48.10        74.20        30.64        52.27 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 
       13.41        24.62        33.47        44.55         0.95        59.84 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       73.22        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       21.24        83.97        49.25        75.06        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4890 
       66.21        61.91        57.83        64.18        51.52        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 
       56.35        49.97        58.92        49.18        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       45.14         3.06        18.81        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-5689 
       18.87        25.25        18.15        62.10        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       60.99        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
      105.93        83.90        18.77        25.45         0.59        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       58.82        18.44        56.94        55.33        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       47.54         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       14.63        22.78        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       37.15        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
        6.77         4.18         7.96        10.29        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       19.43        15.25        10.85        59.01        67.30        75.42 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        35.67        38.99        24.33        31.20 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 
       11.57        18.21        19.63         0.10        35.18         0.23 
TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       29.46        23.28        19.73        12.46         8.28        12.99 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O 
        9.63        58.45        25.08        19.56         7.33        16.87 
TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 
       16.77        10.09        34.49        20.61         2.10         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 
       63.72        22.92        43.20        21.63        40.83        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7048 
       26.04        13.25         7.66        11.97         7.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       44.84        61.28        49.84        26.27        20.12        11.28 
TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G 
       13.78        79.86        54.90        19.00        10.68         0.43 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD 
       48.62        11.05        34.82        25.15        13.68        16.90 
TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U 
       12.92         1.05         0.89         4.60        73.25        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 
       19.99        85.78        67.17        22.26         0.13        30.38 
TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 
       27.65         0.36        12.13        25.97        21.44        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94         6.61        84.95        92.58        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       12.85        27.06        38.63        18.02         0.53        86.27 
TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RZ 
       52.11        26.01        29.00        18.64        18.05         6.74 
TCGA-Y8-A8S1 
       13.28 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.10 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           194.79            129.37 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           28.635            31.330 
[1] "0.1 - 194.8 (28.6)" "0.1 - 129.4 (31.3)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED       190       39        68       48
  7P GAIN WILD-TYPE     258       64       122       52
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I               190               258
  STAGE II               39                64
  STAGE III              68               122
  STAGE IV               48                52
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P GAIN MUTATED   195  51  99   7
  7P GAIN WILD-TYPE 267  72 152   8
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1             195               267
  T2              51                72
  T3              99               152
  T4               7                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7P GAIN MUTATED   118  18   3
  7P GAIN WILD-TYPE 199  25   3
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             118               199
  N1              18                25
  N2               3                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   190  43
  7P GAIN WILD-TYPE 352  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    190   43
  7P GAIN WILD-TYPE  352   46
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             190               352
  1              43                46
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    85 271
  7P GAIN WILD-TYPE 202 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     85  271
  7P GAIN WILD-TYPE  202  301
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              85               202
  MALE               271               301
[1] 2 2
[1] FALSE
D13V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7P GAIN MUTATED                   24                               171
  7P GAIN WILD-TYPE                 42                               353
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7P GAIN MUTATED                                     161
  7P GAIN WILD-TYPE                                   108
D13V9, multiclass
                                       clus
vv                                      7P GAIN MUTATED 7P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                 171               353
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             161               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, continuous
D13V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  2     8
  7P GAIN WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          41   292
  7P GAIN WILD-TYPE                        75   410
D13V12, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          8                 7
  BLACK OR AFRICAN AMERICAN                     41                75
  WHITE                                        292               410
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V13, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    15 252
  7P GAIN WILD-TYPE  27 345
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     15  252
  7P GAIN WILD-TYPE   27  345
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                  15                27
  NOT HISPANIC OR LATINO             252               345
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   265  81
  7Q GAIN WILD-TYPE 367 130
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              346               497 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               81               130 
$`7Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 
       62.37       151.96        49.97        23.47        25.91       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 
        3.55        52.27        11.21        42.35        10.68        74.93 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 
       16.67        80.38        86.10        77.85        57.17        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3336 
       49.08        49.02        48.59        38.99        24.69        34.29 
TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 
       52.93        42.97        10.49        24.16        43.20        18.87 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3425 TCGA-AK-3427 
       65.52        20.28         0.10        11.18       109.91        84.36 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
       66.31        15.78        72.07        67.20        57.37        48.36 
TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 
       45.93         3.32         1.41         4.57         3.48        28.47 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4815 
       19.73         3.16        43.96         3.25        46.59        52.21 
TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4852 
        6.02        10.09        27.42        53.88         6.71        36.85 
TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 
       43.30        10.95         2.24        90.87        19.30        11.80 
TCGA-B0-5116 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 
       21.60        15.78        84.92        56.94        39.55        61.32 
TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 
       35.90        32.98         0.23         0.53         5.46         0.36 
TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5550 
       16.80        17.19        25.55        25.91        23.01        14.27 
TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4166 
       29.88         4.93       111.02        85.51       101.06         0.43 
TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 
       89.36        77.03        62.24        61.78        64.27        97.45 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 
       37.25        15.16         0.07        93.99        62.86        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 
       11.31        33.99        77.98        48.07        13.15         5.33 
TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4799 
       60.59        68.38        15.78        36.53        10.98        37.25 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 
        6.71        47.97        71.41        58.68        60.30         6.74 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 
       58.98        48.89        45.50        14.93        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5009 
       36.95         3.88        16.47        43.00        30.64        36.23 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5198 
        6.35        79.30         1.78         9.63        62.86        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4644 
       34.95        31.27        46.55        63.25        14.17        11.05 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 
       79.66        47.18        74.27        77.36        69.86        30.64 
TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       63.98        59.44        47.67        51.29        49.28        54.48 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5682 
        4.57        63.88        72.00        25.71        22.32        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 
       62.10        73.35        53.42        66.31        74.66         1.35 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
      103.43        18.77        46.16        47.08        69.21         6.77 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
       61.41        23.74        56.28        55.33        47.01        10.85 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5565 
       57.21        22.52         1.94        31.10        67.96        43.69 
TCGA-DV-5574 TCGA-G6-A8L7 TCGA-MM-A564 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 
       66.28        70.13        19.96         7.04        75.55        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL 
      100.27        56.91         4.57        34.85        56.81        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       30.71        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 
        0.13        12.82        61.05        19.13         0.89        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       30.48        25.64        23.97        23.31         0.76        19.63 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       14.33        16.96         8.48        16.31        15.75        12.46 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       76.64        13.55        30.35        44.61        49.25         2.20 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       21.67        24.56         3.55         0.46         6.58        33.83 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 
       17.49        47.80        26.04        25.35        10.88         0.95 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
       11.97         2.76       123.62        48.26        96.92        50.40 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 
      129.86        35.93        37.55        24.46         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
        3.02        40.77        80.88        51.19        61.02        34.19 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       24.89        13.08         2.40         1.18         4.01        51.78 
TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       39.25        25.84         6.38        17.98        17.33        80.65 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DD 
      194.79         3.68        27.65        12.43        17.95        11.21 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y 
       68.12        13.41        11.84        56.75         5.49         2.04 
TCGA-IA-A83T TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
       88.24        21.34        16.34        12.36        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
       11.41        34.29        27.78        20.25        15.48        87.22 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       33.04        28.80        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       38.86        30.67        25.68        27.39        12.99        15.91 
TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        15.62        25.28         6.02 

$`7Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       86.56        66.54        73.91        28.80        54.74        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 
      129.37        87.91        25.48        65.19         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 
       79.04        92.71        87.78       103.27        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        12.16        36.82        47.21         0.53        39.16 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       37.15        49.58        36.36        37.38        48.82        21.86 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       31.07         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       82.32        51.25        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-A6NJ TCGA-A3-A6NL 
       55.76        20.71        18.64        28.31        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 
        0.10        10.62        29.10        73.08        60.92        68.61 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        42.08        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
       40.70         1.41         2.53        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4718 
       65.10         7.82         5.98         2.14         6.64        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       40.44        36.53        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       68.71        40.70        45.30        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       65.29        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       20.94        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       15.09         8.05        21.86        52.08        15.95        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
       90.48        52.54        30.48        29.95        35.90        26.20 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       14.76        79.17       112.80        48.89       101.13        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 
       56.78        60.33        90.12        52.77       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 
      102.48        47.97        96.36        89.49        97.41        32.61 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
       21.57        16.67         9.57         5.75         1.25         4.64 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        23.31        27.16        27.55        25.05        24.66 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60         6.38         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       27.29        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
       16.27        14.17        94.72        90.28        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       99.85        23.05        54.90        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       62.07        80.68        21.21        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4355 
       54.77        49.08        44.94        12.23        12.33        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       71.80        61.68        10.82        61.97        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
       11.64        60.95        48.95        20.38        36.39        36.95 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
        6.94        87.45        63.62        61.22        61.51        57.40 
TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 
       14.24        49.38         7.23        47.11        53.65        36.07 
TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
       33.34        25.81        27.22        46.45         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       35.21        28.87        48.10        74.20        30.64        52.27 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 
       13.41        24.62        33.47        44.55         0.95        59.84 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       73.22        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       21.24        83.97        49.25        75.06        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4890 
       66.21        61.91        57.83        64.18        51.52        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 
       56.35        49.97        58.92        49.18        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 
       45.14         3.06        18.81        79.89        84.66        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       25.25        18.15        67.00        53.26        60.99        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 
        5.39        85.78        73.18        78.18       105.93        83.90 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       25.45         0.59        58.75        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 
       93.04         5.46        63.42        58.82         0.82        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 
       56.94        55.33        10.22        21.76        47.54         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       62.63        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JG 
       15.25        10.85        59.01        67.30        75.42        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y 
       51.52        35.67        38.99        24.33        31.20        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 
       18.21        19.63         0.10        35.18         0.23        29.46 
TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 
       23.28        19.73        12.46         8.28        12.99         9.63 
TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 
       58.45        25.08        19.56         7.33        16.87        16.77 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
       10.09        34.49        20.61         2.10         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 
       22.92        43.20        21.63        40.83        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
       13.25         7.66         7.92        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-DZ-6131 
       49.84        26.27        20.12        11.28        13.78        79.86 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 
       54.90        19.00        10.68         0.43        48.62        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM 
       34.82        25.15        13.68        16.90        12.92         1.05 
TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
        0.89         4.60        73.25        16.80        19.99        85.78 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 
       67.17        22.26         0.13        30.38        27.65         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA 
       12.13        25.97        21.44        99.78        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL 
       84.95        92.58        50.60        78.90        12.85        27.06 
TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 
       38.63        18.02         0.53        86.27        52.11        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       29.00        18.64        18.05         6.74        13.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           194.79            129.37 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           28.145            31.790 
[1] "0.1 - 194.8 (28.1)" "0.1 - 129.4 (31.8)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED       191       37        68       51
  7Q GAIN WILD-TYPE     257       66       122       49
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I               191               257
  STAGE II               37                66
  STAGE III              68               122
  STAGE IV               51                49
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q GAIN MUTATED   196  49 102   7
  7Q GAIN WILD-TYPE 266  74 149   8
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1             196               266
  T2              49                74
  T3             102               149
  T4               7                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  7Q GAIN MUTATED   116  18   3
  7Q GAIN WILD-TYPE 201  25   3
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             116               201
  N1              18                25
  N2               3                 3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   189  46
  7Q GAIN WILD-TYPE 353  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    189   46
  7Q GAIN WILD-TYPE  353   43
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             189               353
  1              46                43
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    87 271
  7Q GAIN WILD-TYPE 200 301
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     87  271
  7Q GAIN WILD-TYPE  200  301
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              87               200
  MALE               271               301
[1] 2 2
[1] FALSE
D14V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7Q GAIN MUTATED                   24                               172
  7Q GAIN WILD-TYPE                 42                               352
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7Q GAIN MUTATED                                     162
  7Q GAIN WILD-TYPE                                   107
D14V9, multiclass
                                       clus
vv                                      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                 172               352
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             162               107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, continuous
D14V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  2     8
  7Q GAIN WILD-TYPE                                0     7
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          41   294
  7Q GAIN WILD-TYPE                        75   408
D14V12, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          8                 7
  BLACK OR AFRICAN AMERICAN                     41                75
  WHITE                                        294               408
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V13, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    15 255
  7Q GAIN WILD-TYPE  27 342
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15  255
  7Q GAIN WILD-TYPE   27  342
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  15                27
  NOT HISPANIC OR LATINO             255               342
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    46  17
  8P GAIN WILD-TYPE 586 194
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               63               780 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               17               194 
$`8P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        98.96        28.11        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-A3-3313 TCGA-A3-3316 
       74.93        80.38        87.78        86.10        24.16        49.08 
TCGA-AK-3433 TCGA-AK-3445 TCGA-B0-4713 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5097 
       72.07        42.08         6.64        10.09        10.29        21.86 
TCGA-B0-5109 TCGA-B4-5832 TCGA-BP-4342 TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-5000 
       19.30         0.23        74.17        13.15        31.30        18.51 
TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4871 TCGA-CJ-4901 TCGA-CJ-4923 TCGA-CW-5588 
       37.22        31.79        79.66        47.67        18.81        66.31 
TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5469 
       74.66        69.21        61.41        56.28        57.21        31.10 
TCGA-CZ-5470 TCGA-CZ-5987 TCGA-MM-A564 TCGA-2Z-A9J2 TCGA-2Z-A9JP TCGA-4A-A93X 
       12.69        14.63        19.96        59.01        29.36        12.82 
TCGA-A4-8630 TCGA-AL-3471 TCGA-B1-A47O TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 
       14.33        13.55        16.87         0.16        43.20        25.35 
TCGA-BQ-7056 TCGA-G7-6789 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-P4-A5EA 
       20.12         4.01         3.68         1.05        22.26         6.61 
TCGA-P4-AAVL TCGA-SX-A71U TCGA-SX-A7SR 
       16.01        33.04        26.47 

$`8P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       103.27        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       39.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        24.69        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       74.63        74.76        24.16        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       60.92        68.61        67.20        57.37        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 
        5.98         2.14        19.73         3.16        43.96         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       14.93        54.48        29.10        78.44        68.71        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         5.75         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       27.02        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       49.25        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 
       54.48        38.56        45.14         3.06         4.57        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       73.18        78.18         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 
       18.77        25.45        46.16         0.59        47.08        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 
       47.54        22.52         2.40         1.94        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        12.26        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       15.25        10.85         7.04        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       24.33        31.20        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.63        19.73        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       76.64        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       19.56         7.33        21.67        24.56         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         6.81        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R 
       16.90        80.65       194.79        12.92        27.65        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 
        2.04        85.78        88.24        67.17        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       84.95        92.58        52.27        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        14.07        47.90        47.44        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       11.93        19.00        38.63        16.31        41.62        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           151.96            194.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            26.47             30.64 
[1] "0.2 - 152.0 (26.5)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.1"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED        18       18        15       11
  8P GAIN WILD-TYPE     430       85       175       89
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                18               430
  STAGE II               18                85
  STAGE III              15               175
  STAGE IV               11                89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P GAIN MUTATED    18  19  24   1
  8P GAIN WILD-TYPE 444 104 227  14
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              18               444
  T2              19               104
  T3              24               227
  T4               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"
                   vv
clus                 N0  N1  N2
  8P GAIN MUTATED    27   6   1
  8P GAIN WILD-TYPE 290  37   5
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              27               290
  N1               6                37
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    34   9
  8P GAIN WILD-TYPE 508  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     34    9
  8P GAIN WILD-TYPE  508   80
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              34               508
  1               9                80
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    20  44
  8P GAIN WILD-TYPE 267 528
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     20   44
  8P GAIN WILD-TYPE  267  528
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              20               267
  MALE                44               528
[1] 2 2
[1] FALSE
D15V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8P GAIN MUTATED                   17                                29
  8P GAIN WILD-TYPE                 49                               495
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8P GAIN MUTATED                                      18
  8P GAIN WILD-TYPE                                   251
D15V9, multiclass
                                       clus
vv                                      8P GAIN MUTATED 8P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 17                49
  KIDNEY CLEAR CELL RENAL CARCINOMA                  29               495
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              18               251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, continuous
D15V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     0
  8P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           3    60
  8P GAIN WILD-TYPE                       113   642
D15V12, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                15
  BLACK OR AFRICAN AMERICAN                      3               113
  WHITE                                         60               642
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V13, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3  43
  8P GAIN WILD-TYPE  39 554
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   43
  8P GAIN WILD-TYPE   39  554
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              43               554
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    66  29
  8Q GAIN WILD-TYPE 566 182
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               95               748 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               29               182 
$`8Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        98.96        28.11        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-A3-3308 TCGA-A3-3313 
       74.93        80.38        87.78        86.10         0.53        24.16 
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3336 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3445 
       49.08        37.15        34.29        72.07        68.61        42.08 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5081 TCGA-B0-5097 
       43.96         6.64        10.09        10.29        11.90        21.86 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B4-5832 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 
       29.95        19.30         0.23        20.91        27.02         0.53 
TCGA-B8-A54I TCGA-BP-4338 TCGA-BP-4342 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4798 
        4.93        93.99        74.17         5.98        13.15        10.98 
TCGA-BP-4799 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5169 
       37.25        58.68        46.45        31.30        18.51         6.35 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5191 TCGA-CJ-4871 TCGA-CJ-4881 
        1.78        30.64        37.22        31.79        79.66        66.21 
TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5677 TCGA-CJ-6033 TCGA-CW-5588 
       47.67        54.48        18.81        25.71         7.36        66.31 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5464 
       74.66        46.16        69.21        61.41        56.28        57.21 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 TCGA-MM-A564 
       22.52         1.94        31.10        12.69        14.63        19.96 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-8630 TCGA-AL-3466 
       59.01        58.22        29.36        12.82        14.33         9.63 
TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-7056 TCGA-F9-A8NY 
       13.55         0.16        43.20        25.35        20.12         1.18 
TCGA-G7-6789 TCGA-G7-6793 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A40Y TCGA-IZ-8195 
        4.01        11.05         3.68         1.05         2.04        22.26 
TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71U TCGA-SX-A7SR 
        6.61        16.01        14.07        33.04        26.47 

$`8Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       103.27        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 
       63.95        12.66        12.16        36.82        47.21        39.16 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.02        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       37.38        48.82        21.86        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 
       73.08        66.31        15.78        60.92        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        40.01        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        2.53         3.48        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73         3.16 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
       36.53        14.93        54.48        29.10        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       11.64        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 
       36.85        70.52        20.94        43.30        11.24         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       30.48        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67         9.57         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       25.91        23.01        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60         6.38        14.27        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 
       80.68        37.25        21.21        15.16         0.07        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98        77.62        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        20.38        36.39        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
       47.97         6.94        87.45        71.41        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       14.93        36.07        33.34        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 
       35.21        36.23        28.87        48.10        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       58.95        11.05        21.24        83.97        49.25        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
       74.27        75.06        77.36        64.27        71.87        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        56.35        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        49.28        50.33        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 
        4.57        63.88        72.00        79.89        84.66        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
       83.77        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       73.18        78.18         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45         0.59        47.08        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 
        2.40        80.19        67.96        65.65        12.26        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
       35.87         2.01        19.43        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       75.55       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       26.43        30.71        24.33        31.20        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       16.18        22.49         0.13        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31         0.76        19.63        19.73        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       58.45        76.64        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        2.40         0.43        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R 
       16.90        80.65       194.79        12.92        27.65        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       85.78        88.24        67.17        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       92.58        52.27        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       38.63        16.31        41.62        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           151.96            194.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            25.91             30.89 
[1] "0.2 - 152.0 (25.9)" "0.1 - 194.8 (30.9)"
[1] "hr=" "1.4"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED        27       21        28       18
  8Q GAIN WILD-TYPE     421       82       162       82
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                27               421
  STAGE II               21                82
  STAGE III              28               162
  STAGE IV               18                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q GAIN MUTATED    27  22  43   2
  8Q GAIN WILD-TYPE 435 101 208  13
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              27               435
  T2              22               101
  T3              43               208
  T4               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  8Q GAIN MUTATED    37  11   2
  8Q GAIN WILD-TYPE 280  32   4
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              37               280
  N1              11                32
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    55  16
  8Q GAIN WILD-TYPE 487  73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     55   16
  8Q GAIN WILD-TYPE  487   73
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              55               487
  1              16                73
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    31  65
  8Q GAIN WILD-TYPE 256 507
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     31   65
  8Q GAIN WILD-TYPE  256  507
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              31               256
  MALE                65               507
[1] 2 2
[1] FALSE
D16V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8Q GAIN MUTATED                   17                                56
  8Q GAIN WILD-TYPE                 49                               468
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8Q GAIN MUTATED                                      23
  8Q GAIN WILD-TYPE                                   246
D16V9, multiclass
                                       clus
vv                                      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 17                49
  KIDNEY CLEAR CELL RENAL CARCINOMA                  56               468
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              23               246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V10, continuous
D16V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     2
  8Q GAIN WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           6    86
  8Q GAIN WILD-TYPE                       110   616
D16V12, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                      6               110
  WHITE                                         86               616
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V13, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     4  62
  8Q GAIN WILD-TYPE  38 535
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   62
  8Q GAIN WILD-TYPE   38  535
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                38
  NOT HISPANIC OR LATINO              62               535
[1] 2 2
[1] FALSE

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                 0   1
  9P GAIN MUTATED    20   6
  9P GAIN WILD-TYPE 612 205
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               817 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               205 
$`9P GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8428 
      137.06        98.96        24.79       151.96        49.97        52.27 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 
       74.93        80.38        77.85        43.20        66.31        72.07 
TCGA-AK-3440 TCGA-BP-4331 TCGA-BP-4770 TCGA-BP-4969 TCGA-BP-5181 TCGA-CJ-4870 
       57.37        80.68        10.82        58.98        49.15        49.25 
TCGA-CJ-4884 TCGA-CJ-4897 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5468 TCGA-B3-4104 
       57.83        59.44        61.41        55.33         1.94        34.49 
TCGA-BQ-7058 TCGA-GL-7966 
       11.28         3.68 

$`9P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.99        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       92.71        16.67        87.78       103.27        86.10        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        83.97        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       57.21        47.54        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        10.09        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        20.12         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.33        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.94              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           151.96            194.79 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            57.60             29.88 
[1] "1.9 - 152.0 (57.6)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.6"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         7        9         7        3
  9P GAIN WILD-TYPE     441       94       183       97
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 7               441
  STAGE II                9                94
  STAGE III               7               183
  STAGE IV                3                97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P GAIN MUTATED     7   9   9   1
  9P GAIN WILD-TYPE 455 114 242  14
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               7               455
  T2               9               114
  T3               9               242
  T4               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"
                   vv
clus                 N0  N1  N2
  9P GAIN MUTATED    13   1   2
  9P GAIN WILD-TYPE 304  42   4
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              13               304
  N1               1                42
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    21   1
  9P GAIN WILD-TYPE 521  88
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     21    1
  9P GAIN WILD-TYPE  521   88
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              21               521
  1               1                88
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15  11
  9P GAIN WILD-TYPE 272 561
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15   11
  9P GAIN WILD-TYPE  272  561
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              15               272
  MALE                11               561
[1] 2 2
[1] FALSE
D17V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9P GAIN MUTATED                    9                                14
  9P GAIN WILD-TYPE                 57                               510
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9P GAIN MUTATED                                       3
  9P GAIN WILD-TYPE                                   266
D17V9, multiclass
                                       clus
vv                                      9P GAIN MUTATED 9P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  14               510
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               3               266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, continuous
D17V11, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                65 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-A3-A8OV        TCGA-A3-A8OW 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-DV-A4W0        TCGA-G6-A8L7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JD        TCGA-2Z-A9JI        TCGA-2Z-A9JN 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-5561 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"9P GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     1
  9P GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           2    23
  9P GAIN WILD-TYPE                       114   679
D17V12, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      2               114
  WHITE                                         23               679
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V13, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  19
  9P GAIN WILD-TYPE  40 578
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   19
  9P GAIN WILD-TYPE   40  578
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              19               578
[1] 2 2
[1] FALSE

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    17   7
  9Q GAIN WILD-TYPE 615 204
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               819 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               204 
$`9Q GAIN MUTATED`
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8428 
      137.06        98.96        24.79       151.96        49.97        52.27 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 
       74.93        80.38        77.85        43.20        66.31        72.07 
TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4698 TCGA-BP-4770 TCGA-BP-4969 TCGA-CJ-4884 
       57.37         3.32         1.38        10.82        58.98        57.83 
TCGA-CJ-4897 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5468 TCGA-BQ-7058 TCGA-GL-7966 
       59.44        61.41        55.33         1.94        11.28         3.68 

$`9Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       47.24       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.99        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       92.71        16.67        87.78       103.27        86.10        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67         9.57         5.75         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       56.28        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       21.76        57.21        47.54        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       22.49         0.13        12.82        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        20.12         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             1.38              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           151.96            194.79 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            57.60             30.25 
[1] "1.4 - 152.0 (57.6)" "0.1 - 194.8 (30.2)"
[1] "hr=" "1.2"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         5        8         6        5
  9Q GAIN WILD-TYPE     443       95       184       95
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 5               443
  STAGE II                8                95
  STAGE III               6               184
  STAGE IV                5                95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q GAIN MUTATED     5   8   8   3
  9Q GAIN WILD-TYPE 457 115 243  12
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               5               457
  T2               8               115
  T3               8               243
  T4               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"
                   vv
clus                 N0  N1  N2
  9Q GAIN MUTATED    13   1   2
  9Q GAIN WILD-TYPE 304  42   4
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              13               304
  N1               1                42
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    18   2
  9Q GAIN WILD-TYPE 524  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     18    2
  9Q GAIN WILD-TYPE  524   87
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              18               524
  1               2                87
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    13  11
  9Q GAIN WILD-TYPE 274 561
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13   11
  9Q GAIN WILD-TYPE  274  561
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              13               274
  MALE                11               561
[1] 2 2
[1] FALSE
D18V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9Q GAIN MUTATED                    9                                13
  9Q GAIN WILD-TYPE                 57                               511
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9Q GAIN MUTATED                                       2
  9Q GAIN WILD-TYPE                                   267
D18V9, multiclass
                                       clus
vv                                      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  13               511
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, continuous
D18V11, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                65 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345        TCGA-KM-8639 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KN-8433        TCGA-KO-8408        TCGA-A3-A8OV        TCGA-A3-A8OW 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-DV-A4W0        TCGA-G6-A8L7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-MM-A84U        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JD        TCGA-2Z-A9JI        TCGA-2Z-A9JN 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-5561 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9        TCGA-Q2-A5QZ 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PO 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PX        TCGA-WN-A9G9 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ 
"9Q GAIN WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1    22
  9Q GAIN WILD-TYPE                       115   680
D18V12, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      1               115
  WHITE                                         22               680
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V13, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  18
  9Q GAIN WILD-TYPE  40 579
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   18
  9Q GAIN WILD-TYPE   40  579
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              18               579
[1] 2 2
[1] FALSE

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                  0   1
  10P GAIN MUTATED    21   7
  10P GAIN WILD-TYPE 611 204
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                28                815 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                204 
$`10P GAIN MUTATED`
TCGA-KL-8324 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8436 TCGA-A3-3316 TCGA-AK-3453 
      141.73         0.99        11.21        42.35        49.08        45.93 
TCGA-B0-4690 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4338 TCGA-BP-4342 
        1.41        19.30         0.23         5.46        93.99        74.17 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 TCGA-CZ-4854 TCGA-CZ-4858 
       13.15        68.38        30.64        66.31        46.16        69.21 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-EU-5905 TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 
       61.41        23.74         3.91        29.46        76.64         1.15 
TCGA-BQ-5882 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-SX-A7SS 
       21.63        13.08         1.18        48.30 

$`10P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       39.16        24.16        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        60.92        72.07        68.61        67.20        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         3.32         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       29.95        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67         9.57         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
       15.16         0.07        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       48.10         6.35        79.30         1.78        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
      105.93        83.90       103.43        18.77        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 
       93.04         5.46        63.42        58.82         0.82        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       23.90        66.02        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       56.81        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        58.45        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       50.50        28.18        26.40        20.61         0.46        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89        10.68         2.40         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       13.68        25.84         6.38        17.98        17.33        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU 
       19.00        38.63        16.31        41.62        26.47        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.23               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            141.73             194.79 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             30.05              30.48 
[1] "0.2 - 141.7 (30.1)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED        11        7         6        4
  10P GAIN WILD-TYPE     437       96       184       96
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                 11                437
  STAGE II                 7                 96
  STAGE III                6                184
  STAGE IV                 4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P GAIN MUTATED    12   8   6   3
  10P GAIN WILD-TYPE 450 115 245  12
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               12                450
  T2                8                115
  T3                6                245
  T4                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"
                    vv
clus                  N0  N1  N2
  10P GAIN MUTATED     9   4   0
  10P GAIN WILD-TYPE 308  39   6
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                9                308
  N1                4                 39
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    22   3
  10P GAIN WILD-TYPE 520  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     22    3
  10P GAIN WILD-TYPE  520   86
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               22                520
  1                3                 86
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    10  19
  10P GAIN WILD-TYPE 277 553
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     10   19
  10P GAIN WILD-TYPE  277  553
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               10                277
  MALE                 19                553
[1] 2 2
[1] FALSE
D19V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10P GAIN MUTATED                    4                                17
  10P GAIN WILD-TYPE                 62                               507
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10P GAIN MUTATED                                       8
  10P GAIN WILD-TYPE                                   261
D19V9, multiclass
                                       clus
vv                                      10P GAIN MUTATED 10P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                   17                507
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                8                261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, continuous
D19V11, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 65 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KO-8408 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-KO-8409         TCGA-A3-A8OV         TCGA-A3-A8OW 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-DV-A4W0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P GAIN MUTATED                                  0     2
  10P GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2    23
  10P GAIN WILD-TYPE                       114   679
D19V12, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          23                679
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V13, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  18
  10P GAIN WILD-TYPE  42 579
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   18
  10P GAIN WILD-TYPE   42  579
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               18                579
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    16   6
  10Q GAIN WILD-TYPE 616 205
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                821 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                205 
$`10Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KN-8427 TCGA-AK-3453 TCGA-B0-5109 TCGA-B4-5832 TCGA-BP-4352 
      141.73         0.99        45.93        19.30         0.23        11.31 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 TCGA-CZ-4854 TCGA-CZ-4858 
       13.15        68.38        30.64        66.31        46.16        69.21 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-EU-5905 TCGA-A4-8098 TCGA-AL-3468 TCGA-B9-4617 
       61.41        23.74         3.91        29.46        76.64         1.15 
TCGA-BQ-5882 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-SX-A7SS 
       21.63        13.08         1.18        48.30 

$`10Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        29.95        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       11.80        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         5.75         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       48.10         6.35        79.30         1.78        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
      105.93        83.90       103.43        18.77        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 
       93.04         5.46        63.42        58.82         0.82        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       23.90        66.02        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       56.81        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        58.45        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       50.50        28.18        26.40        20.61         0.46        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 
       19.00        24.89        10.68         2.40         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       13.68        25.84         6.38        17.98        17.33        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU 
       19.00        38.63        16.31        41.62        26.47        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.23               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            141.73             194.79 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             26.60              30.58 
[1] "0.2 - 141.7 (26.6)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED        10        4         3        4
  10Q GAIN WILD-TYPE     438       99       187       96
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                 10                438
  STAGE II                 4                 99
  STAGE III                3                187
  STAGE IV                 4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED    11   5   4   2
  10Q GAIN WILD-TYPE 451 118 247  13
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               11                451
  T2                5                118
  T3                4                247
  T4                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10Q GAIN MUTATED     7   3   0
  10Q GAIN WILD-TYPE 310  40   6
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                7                310
  N1                3                 40
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    17   3
  10Q GAIN WILD-TYPE 525  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     17    3
  10Q GAIN WILD-TYPE  525   86
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               17                525
  1                3                 86
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     9  13
  10Q GAIN WILD-TYPE 278 559
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      9   13
  10Q GAIN WILD-TYPE  278  559
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                9                278
  MALE                 13                559
[1] 2 2
[1] FALSE
D20V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10Q GAIN MUTATED                    2                                13
  10Q GAIN WILD-TYPE                 64                               511
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10Q GAIN MUTATED                                       7
  10Q GAIN WILD-TYPE                                   262
D20V9, multiclass
                                       clus
vv                                      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   13                511
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                7                262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                 89 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KO-8416         TCGA-A3-A8CQ         TCGA-A3-A8OV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-4621 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MM-A563         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JK         TCGA-2Z-A9JM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-2Z-A9JQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-8310 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4115         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A69E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7963 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DD         TCGA-HE-A5NI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IZ-A6M8         TCGA-MH-A854 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-Y8-A894         TCGA-Y8-A896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V11, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 66 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-A3-A8OV 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-5158 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MM-A84U         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         TCGA-2Z-A9JI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-4A-A93W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-A48D         TCGA-A4-A57E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3472         TCGA-AL-7173 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4117         TCGA-B9-A69E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7963         TCGA-F9-A97G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           2    17
  10Q GAIN WILD-TYPE                       114   685
D20V12, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          17                685
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V13, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  15
  10Q GAIN WILD-TYPE  42 582
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   15
  10Q GAIN WILD-TYPE   42  582
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               15                582
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    40  15
  11P GAIN WILD-TYPE 592 196
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                55                788 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                196 
$`11P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8339 TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 
      141.73        28.11        24.79       151.96        23.47        25.91 
TCGA-KN-8425 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      104.52        11.21        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 
       77.85        57.17        24.16        24.16        72.07        57.37 
TCGA-AK-3453 TCGA-B0-4710 TCGA-B0-4844 TCGA-B0-5113 TCGA-B4-5832 TCGA-B8-4620 
       45.93         3.16        10.29        11.80         0.23        25.55 
TCGA-B8-A54I TCGA-BP-4167 TCGA-BP-4337 TCGA-BP-4351 TCGA-BP-4799 TCGA-BP-4994 
        4.93        89.36         0.07        31.89        37.25        43.00 
TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4885 
       37.22        34.95        46.55        11.05        79.66        69.86 
TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 
       49.28        22.32        61.91        69.21         6.77        61.41 
TCGA-CZ-5460 TCGA-CZ-5468 TCGA-EU-5905 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B9-4117 
       47.01         1.94         3.91         8.48        49.25         0.46 
TCGA-BQ-5889 TCGA-BQ-5892 TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5EA 
       10.88        11.97        13.08        17.33         3.68         6.61 
TCGA-P4-A5EB 
       84.95 

$`11P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       87.91        25.48        65.19         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33         2.50        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
      103.27        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       47.21         0.53        39.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       43.20        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
       66.31        15.78        60.92        68.61        67.20        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       48.36        42.08        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 
        7.82         5.98         2.14        19.73        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        11.64        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       35.90        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        9.57         5.75         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        17.19        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        21.21        15.16        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        44.55        31.27         0.95        59.84 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       53.52        58.95        21.24        83.97        49.25        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        57.83        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       84.66        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       46.16         0.59        47.08        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       23.90        66.02        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       56.81        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       12.46        16.96        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        44.61         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 
       50.50        28.18        26.40        20.61         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
       26.04        30.28        26.04        25.35        13.25         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        10.68         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            151.96             194.79 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             31.89              30.48 
[1] "0.1 - 152.0 (31.9)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1"  
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED        18        9        17       12
  11P GAIN WILD-TYPE     430       94       173       88
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                 18                430
  STAGE II                 9                 94
  STAGE III               17                173
  STAGE IV                12                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P GAIN MUTATED    18  11  27   1
  11P GAIN WILD-TYPE 444 112 224  14
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               18                444
  T2               11                112
  T3               27                224
  T4                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"
                    vv
clus                  N0  N1  N2
  11P GAIN MUTATED    23   5   1
  11P GAIN WILD-TYPE 294  38   5
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               23                294
  N1                5                 38
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    32  11
  11P GAIN WILD-TYPE 510  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     32   11
  11P GAIN WILD-TYPE  510   78
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               32                510
  1               11                 78
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    21  36
  11P GAIN WILD-TYPE 266 536
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     21   36
  11P GAIN WILD-TYPE  266  536
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               21                266
  MALE                 36                536
[1] 2 2
[1] FALSE
D21V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11P GAIN MUTATED                   15                                31
  11P GAIN WILD-TYPE                 51                               493
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11P GAIN MUTATED                                      11
  11P GAIN WILD-TYPE                                   258
D21V9, multiclass
                                       clus
vv                                      11P GAIN MUTATED 11P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  15                 51
  KIDNEY CLEAR CELL RENAL CARCINOMA                   31                493
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               11                258
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V10, continuous
D21V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     2
  11P GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           4    51
  11P GAIN WILD-TYPE                       112   651
D21V12, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       4                112
  WHITE                                          51                651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V13, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     4  38
  11P GAIN WILD-TYPE  38 559
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4   38
  11P GAIN WILD-TYPE   38  559
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               38                559
[1] 2 2
[1] FALSE

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED    42  12
  11Q GAIN WILD-TYPE 590 199
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                54                789 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                199 
$`11Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8339 TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 
      141.73        28.11        24.79       151.96        23.47        25.91 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
      104.52         3.55        11.21        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 
       86.10        77.85        57.17        24.16        24.16        72.07 
TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 TCGA-B0-4844 TCGA-B0-5113 TCGA-B2-4099 
       57.37        45.93         3.16        10.29        11.80        12.30 
TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 TCGA-BP-4337 TCGA-BP-4351 TCGA-BP-4799 
       25.55         4.93        89.36         0.07        31.89        37.25 
TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 
       43.00        37.22        34.95        46.55        11.05        79.66 
TCGA-CJ-4885 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CZ-4858 TCGA-CZ-4866 
       69.86        49.28        22.32        61.91        69.21        61.41 
TCGA-CZ-5460 TCGA-EU-5905 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B9-4117 TCGA-BQ-5892 
       47.01         3.91         8.48        49.25         0.46        11.97 
TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-Q2-A5QZ 
       13.08        17.33         3.68         6.61        84.95        14.07 

$`11Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       30.25        44.84        86.56        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       28.80        54.74        62.37        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       87.91        25.48        65.19         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
       19.33         2.50        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       76.90        10.68        79.04        92.71        16.67       103.27 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       42.08        40.01        58.49        48.69        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14        19.73        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       11.64        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       32.61        35.90         1.68        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        17.19        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         1.74         8.42        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
      101.06        93.34        32.61        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       21.21        15.16        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       62.86        54.77        49.08        44.94        12.23        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       19.82        44.55        31.27         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       58.95        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        18.87        25.25        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        66.02        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       30.35        25.08        44.61         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       10.16        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        10.68         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       87.22        42.94        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       78.90        12.85        17.75        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            151.96             194.79 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             33.42              30.48 
[1] "0.1 - 152.0 (33.4)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1.2"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED        19        9        16       10
  11Q GAIN WILD-TYPE     429       94       174       90
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                 19                429
  STAGE II                 9                 94
  STAGE III               16                174
  STAGE IV                10                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q GAIN MUTATED    19  11  25   0
  11Q GAIN WILD-TYPE 443 112 226  15
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               19                443
  T2               11                112
  T3               25                226
  T4                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"
                    vv
clus                  N0  N1  N2
  11Q GAIN MUTATED    22   3   1
  11Q GAIN WILD-TYPE 295  40   5
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               22                295
  N1                3                 40
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    32   9
  11Q GAIN WILD-TYPE 510  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     32    9
  11Q GAIN WILD-TYPE  510   80
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               32                510
  1                9                 80
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    22  33
  11Q GAIN WILD-TYPE 265 539
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     22   33
  11Q GAIN WILD-TYPE  265  539
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               22                265
  MALE                 33                539
[1] 2 2
[1] FALSE
D22V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11Q GAIN MUTATED                   16                                29
  11Q GAIN WILD-TYPE                 50                               495
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11Q GAIN MUTATED                                      10
  11Q GAIN WILD-TYPE                                   259
D22V9, multiclass
                                       clus
vv                                      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  16                 50
  KIDNEY CLEAR CELL RENAL CARCINOMA                   29                495
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               10                259
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, continuous
D22V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     2
  11Q GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           5    48
  11Q GAIN WILD-TYPE                       111   654
D22V12, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       5                111
  WHITE                                          48                654
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V13, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  36
  11Q GAIN WILD-TYPE  38 561
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   36
  11Q GAIN WILD-TYPE   38  561
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               36                561
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   172  64
  12P GAIN WILD-TYPE 460 147
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               236                607 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                64                147 
$`12P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8343 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        71.41        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
      151.96        49.97        23.47        25.91         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       52.27        42.35        80.38        87.78        86.10        77.85 
TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 
       39.16        37.15        24.69        52.93        42.97        24.16 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3433 
       43.20        18.87        20.28       109.91        15.78        72.07 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       67.20        57.37        45.93         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        2.53         1.38         3.62        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        6.64        46.59        52.21         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5081 
       14.93        10.09        27.42        29.03        20.94        11.90 
TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5113 
        7.30        10.95         8.05        30.48        19.30        11.80 
TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 TCGA-B4-5838 
       21.60        56.78        60.33        61.32         0.23         5.46 
TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54F 
       23.31        25.91        23.01        27.02         0.53        17.06 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4176 
        4.93       101.06        93.34        89.36        61.78        64.27 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 
        0.07        93.99        31.89        11.31         5.98        13.15 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4963 
       11.64        15.78         6.71        47.97        71.41        60.30 
TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4992 
       61.22        14.93        46.45        31.30        27.22        16.47 
TCGA-BP-4994 TCGA-BP-5009 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5185 
       43.00        36.23         1.78        30.64        62.86        37.22 
TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5200 TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4872 
       31.79        13.41        34.95        63.25        14.17        47.18 
TCGA-CJ-4873 TCGA-CJ-4884 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4920 
       74.27        57.83        51.29        49.28        54.48         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 
       18.81        63.88        84.66        22.32        61.91        73.35 
TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4856 
       53.42        66.31        74.66         1.35        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
       47.08        61.41        56.28        10.85        57.21        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-EU-5905 TCGA-2K-A9WE 
        1.94        31.10        67.96        14.63         3.91         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG TCGA-2Z-A9JL 
       75.55        59.01       100.27        56.91        54.64        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JT TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 
       30.71        22.49        18.21        19.13        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5DU 
       25.64         0.76        19.63        19.73        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-A47N 
       15.75        12.46        76.64        13.55        44.61        24.56 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 
        0.46        33.83        10.16        50.50        28.18         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 
       43.99        22.06        19.23         0.16        17.49         8.88 
TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7059 
       43.20        25.35        10.88         0.95        11.97         7.63 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 
        7.17         3.81        13.61        37.55         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-F9-A7Q0 TCGA-F9-A8NY 
       40.77        80.88        51.19        61.02        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
        4.01        39.25         6.38        17.98        17.33        16.90 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
      194.79         3.68         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       11.21        68.12        11.84        56.75         5.49        16.80 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-KV-A6GD TCGA-KV-A6GE 
        2.04        85.78        88.24        67.17        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 
       11.41        34.29        27.78        30.38        20.25         0.36 
TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71U 
       84.95        52.27        16.01        12.85        17.75        33.04 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PP 
       28.80        11.93        41.62        26.47        48.30         0.53 
TCGA-UZ-A9PX TCGA-Y8-A8RY 
       27.39        25.28 

$`12P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        24.79        73.91        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
       31.33       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       16.67       103.27        57.17        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
       12.16        36.82        47.21         0.53        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       49.02        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 
       48.82        21.86        34.29        31.07         4.50        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       29.92        18.44        88.37        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       28.70        74.63        74.76        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.64        28.31        65.52        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
        0.10        11.18        10.62        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       66.31        60.92        68.61        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       40.01        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        28.47        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        2.14         3.25        20.25        15.72         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       45.07        33.50        16.77        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        40.70        45.30        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
       11.64        10.29        65.29        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 
       36.85        70.52        43.30        11.24        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       15.09         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
       90.87        90.48        52.54        29.95        35.90        26.20 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       46.68        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        9.57         5.75         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
       17.19        25.55        20.91        23.74         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        17.16        16.60         6.38        14.27        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       14.30        27.29        29.88         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
       90.28        32.61        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       62.24        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       56.91        68.38        60.95        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 
       36.39        10.98        37.25        36.95         6.94        87.45 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       63.62        58.68        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
       53.65        36.07        33.34        25.81        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       46.45         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       38.70        37.02        27.62        37.48        35.21        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10         6.35        79.30        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 TCGA-BP-5196 
       13.35        27.02        33.24        23.47        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        31.27         0.95        59.84        46.55 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       73.22        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 
       11.05        21.24        83.97        49.25        79.66        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 
       77.36        64.27        71.87        66.21        61.91        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        47.67        49.97        58.92        49.18        50.33 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
       38.56        45.14         3.06        72.00        79.89        25.71 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-5689 
       18.87        25.25        18.15        62.10        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       60.99        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 
      105.93        83.90       103.43        18.77        25.45        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       55.33        56.94        55.33        47.01        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       47.54         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       58.22         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        35.67        38.99        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       25.58         5.29        16.18         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7734 TCGA-A4-7915 
       19.63        61.05         0.10        35.18         0.89         0.23 
TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A48D 
       16.64        23.97        23.28        23.31        14.33        12.46 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.48         8.28        12.99         9.63        58.45        30.35 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4103 
       16.87         3.55        16.77         6.58        10.09        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5155 
       34.49        12.46        26.40        20.61         0.46        15.12 
TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        2.10         6.81        14.86        12.30        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        26.04        13.25         7.66         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7060 
       50.40        49.84        26.27        20.12        11.28         7.04 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 
       11.61       129.86        35.93        24.46        13.78         3.02 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       79.86        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 
        2.40         0.43        51.78        48.62        11.05        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
       25.15        13.68        25.84        80.65        12.92        27.65 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
        4.60        13.41        73.25        19.99        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 
       16.34        12.36         0.13        27.65        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       92.58        50.60        78.90        14.07        47.90        47.44 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SU TCGA-UN-AAZ9 
       27.06        19.00        38.63        16.31        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.64        18.05        15.62         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            194.79             129.86 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             26.17              33.34 
[1] "0.1 - 194.8 (26.2)" "0.1 - 129.9 (33.3)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED       117       28        53       39
  12P GAIN WILD-TYPE     331       75       137       61
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                117                331
  STAGE II                28                 75
  STAGE III               53                137
  STAGE IV                39                 61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED   122  33  79   7
  12P GAIN WILD-TYPE 340  90 172   8
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1              122                340
  T2               33                 90
  T3               79                172
  T4                7                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12P GAIN MUTATED    85  20   2
  12P GAIN WILD-TYPE 232  23   4
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               85                232
  N1               20                 23
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   129  33
  12P GAIN WILD-TYPE 413  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    129   33
  12P GAIN WILD-TYPE  413   56
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              129                413
  1               33                 56
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    64 181
  12P GAIN WILD-TYPE 223 391
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     64  181
  12P GAIN WILD-TYPE  223  391
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               64                223
  MALE                181                391
[1] 2 2
[1] FALSE
D23V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12P GAIN MUTATED                   19                               119
  12P GAIN WILD-TYPE                 47                               405
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12P GAIN MUTATED                                     107
  12P GAIN WILD-TYPE                                   162
D23V9, multiclass
                                       clus
vv                                      12P GAIN MUTATED 12P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  19                 47
  KIDNEY CLEAR CELL RENAL CARCINOMA                  119                405
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              107                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, continuous
D23V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     4
  12P GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          29   203
  12P GAIN WILD-TYPE                        87   499
D23V12, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                 11
  BLACK OR AFRICAN AMERICAN                      29                 87
  WHITE                                         203                499
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V13, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7 183
  12P GAIN WILD-TYPE  35 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7  183
  12P GAIN WILD-TYPE   35  414
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 35
  NOT HISPANIC OR LATINO              183                414
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   174  66
  12Q GAIN WILD-TYPE 458 145
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               240                603 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                66                145 
$`12Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8343 
      141.73       137.06        98.96        28.11        24.79        71.41 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 
       62.37       151.96        49.97        23.47        25.91         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 
        0.99        52.27        11.21        42.35        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 
       86.10        77.85        39.16        37.15        24.69        52.93 
TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 
       42.97        24.16        43.20        18.87        20.28       109.91 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 
       15.78        72.07        67.20        57.37        45.93         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 
        1.41         4.57         2.53        28.47         1.38         3.62 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4815 
       19.73         3.16        43.96         6.64        46.59        52.21 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4838 
        6.02        40.44        36.53        14.93        10.09        27.42 
TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5095 
       29.03        20.94        11.90         7.30        10.95         8.05 
TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 
       30.48        19.30        11.80        21.60        56.78        60.33 
TCGA-B0-5713 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-4622 
       61.32         0.23         5.46        23.31        25.91        23.01 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54F TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 
       27.02         0.53        17.06         4.93       101.06        93.34 
TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 
       89.36        61.78        64.27         0.07        93.99        31.89 
TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4803 
       11.31         5.98        13.15        11.64        15.78         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 
       47.97        71.41        60.30        61.22        14.93        46.45 
TCGA-BP-4985 TCGA-BP-4988 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5009 TCGA-BP-5173 
       31.30        27.22        16.47        43.00        36.23         1.78 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5200 
       30.64        62.86        37.22        31.79        13.41        34.95 
TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4884 
       63.25        14.17        47.18        74.27        66.21        57.83 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       51.29        49.28        54.48         4.57        18.81        63.88 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 
       84.66        22.32        61.91        73.35        53.42        66.31 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4866 
       74.66         1.35        46.16         0.59        47.08        61.41 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       56.28        10.85        57.21        22.52         1.94        31.10 
TCGA-CZ-5984 TCGA-CZ-5987 TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       67.96        14.63         3.91         7.04        75.55        59.01 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JT 
      100.27        56.91        54.64        26.43        30.71        22.49 
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
       18.21        19.13        30.48        29.46        25.64         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       19.63        19.73        16.96        16.31        15.75        12.46 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 
       76.64        13.55        44.61        24.56         0.46        33.83 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       10.16        50.50        28.18         1.15        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 
       19.23         0.16        17.49         8.88        43.20        25.35 
TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 
       10.88         0.95        11.97         7.63         7.17         3.81 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 
       13.61        37.55         3.75        14.63        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 
       51.19        61.02        13.08         1.18         4.01        39.25 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 
        6.38        17.98        17.33        16.90       194.79         3.68 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
        1.05        12.43        17.95         0.89        11.21        68.12 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S 
       11.84        56.75         5.49        16.80         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       88.24        67.17        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB TCGA-P4-AAVK 
       27.78        30.38        20.25         0.36        84.95        52.27 
TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       16.01        12.85        17.75        33.04        28.80        11.93 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-Y8-A8RY 
       41.62        26.47        48.30         0.53        27.39        25.28 

$`12Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 
       86.56        66.54        73.91        28.80        54.74        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 
      129.37        87.91        25.48        65.19       104.52        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
       10.68        74.93        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
       47.21         0.53        24.16        49.08        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       34.29        31.07         4.50        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       74.76        53.29        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       65.52        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
       10.62        29.10        84.36        73.08        66.31        60.92 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       68.61        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4694 TCGA-B0-4697 
       28.04        12.13        40.70         1.41         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 
       65.10         7.82         5.98         2.14         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       15.72         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        78.44        68.71        40.70        45.30 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 
       39.45        26.07         2.27        36.85        70.52        43.30 
TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 
       11.24        25.32        18.51        15.09         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       29.95        35.90        26.20        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 
       48.89       101.13        15.78        46.68        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       47.97        96.36        89.49        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         5.75         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 
       27.55        25.05        24.66        17.19        25.55        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74         1.18         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        14.27        34.39        14.30        27.29        29.88 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 
      111.02        85.51        94.72        90.28        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 
        0.43        23.05        77.03        62.24        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       21.21        15.16        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       31.33        12.30        72.59        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        68.38        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4965 
       36.95         6.94        87.45        63.62        58.68        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 
       45.50         7.23        47.11        53.65        36.07        33.34 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 
       25.81        36.95         3.88        46.45         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       37.48        35.21        28.87        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       74.20        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5192 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 
       23.47        24.62        33.47        19.82        44.55        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95        59.84        46.55        73.22        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       49.25        79.66        75.06        77.36        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       61.91        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 
       59.44        50.24        56.35        47.67        49.97        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5672 
       49.18        50.33        38.56        45.14         3.06        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       79.89        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        60.99        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       73.18        78.18       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       25.45        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        55.33        56.94        55.33        47.01 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       10.22        21.76        47.54         2.40        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        12.26        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       23.90        66.02        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       15.25        10.85        58.22         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN 
       34.85        56.81        51.52        35.67        38.99        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W 
       31.20        29.36        25.58         5.29        16.18         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        19.63        61.05         0.10        35.18 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
        0.89         0.23        16.64        23.97        23.28        23.31 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 
       14.33        12.46         8.48         8.28        12.99         9.63 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       58.45        30.35        25.08        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 
        7.33        21.67        16.87         3.55        16.77         6.58 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 
       10.09        30.58        34.49        12.46        26.40        20.61 
TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI 
        0.46        15.12         2.10         6.81        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 
       86.76        19.27        63.72        22.92        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
       40.83        26.04        30.28        26.04        13.25         7.66 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7060 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
       11.28         7.04        11.61       129.86        35.93        24.46 
TCGA-DW-7839 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       13.78         3.02        79.86        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       24.89        10.68         2.40         0.43        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE 
       11.05        34.82        25.15        13.68        25.84        80.65 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X 
       12.92        27.65         4.60        13.41        73.25        19.99 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A561 
       22.26        21.34        16.34        12.36         0.13        27.65 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       42.94         6.61        92.58        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       47.90        47.44        27.06        19.00        38.63        16.31 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       43.76        18.02        60.03        14.83        21.93        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       38.86        52.11        30.67        25.68        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            194.79             129.86 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             26.17              33.47 
[1] "0.1 - 194.8 (26.2)" "0.1 - 129.9 (33.5)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED       117       28        56       40
  12Q GAIN WILD-TYPE     331       75       134       60
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                117                331
  STAGE II                28                 75
  STAGE III               56                134
  STAGE IV                40                 60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q GAIN MUTATED   122  33  83   7
  12Q GAIN WILD-TYPE 340  90 168   8
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1              122                340
  T2               33                 90
  T3               83                168
  T4                7                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  12Q GAIN MUTATED    86  20   3
  12Q GAIN WILD-TYPE 231  23   3
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               86                231
  N1               20                 23
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   132  33
  12Q GAIN WILD-TYPE 410  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    132   33
  12Q GAIN WILD-TYPE  410   56
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              132                410
  1               33                 56
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    65 184
  12Q GAIN WILD-TYPE 222 388
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     65  184
  12Q GAIN WILD-TYPE  222  388
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               65                222
  MALE                184                388
[1] 2 2
[1] FALSE
D24V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12Q GAIN MUTATED                   21                               121
  12Q GAIN WILD-TYPE                 45                               403
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12Q GAIN MUTATED                                     107
  12Q GAIN WILD-TYPE                                   162
D24V9, multiclass
                                       clus
vv                                      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  121                403
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              107                162
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, continuous
D24V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     5
  12Q GAIN WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          29   206
  12Q GAIN WILD-TYPE                        87   496
D24V12, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           5                 10
  BLACK OR AFRICAN AMERICAN                      29                 87
  WHITE                                         206                496
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V13, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     7 186
  12Q GAIN WILD-TYPE  35 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7  186
  12Q GAIN WILD-TYPE   35  411
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 35
  NOT HISPANIC OR LATINO              186                411
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    42   8
  13Q GAIN WILD-TYPE 590 203
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                50                793 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                203 
$`13Q GAIN MUTATED`
TCGA-KN-8419 TCGA-KN-8436 TCGA-A3-3325 TCGA-AK-3453 TCGA-B0-4706 TCGA-B0-4710 
       23.47        42.35        24.69        45.93         2.14         3.16 
TCGA-B0-5690 TCGA-B2-5639 TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4983 TCGA-BP-5198 
       79.17        32.98         0.43        37.25        46.45        19.82 
TCGA-BP-5200 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 
       34.95        49.18        49.28        54.48        63.88        84.66 
TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-DV-5574 
       61.91        53.26        47.01        10.85        57.21        66.28 
TCGA-2Z-A9J1 TCGA-4A-A93X TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A5Y1 
       75.55        12.82        23.97        19.73        14.33        12.99 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5882 
        2.20        19.56        12.46         0.46         1.15        21.63 
TCGA-BQ-5885 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DZ-6133 TCGA-EV-5903 TCGA-G7-6790 
       30.28        96.92        13.61        51.19        24.89        51.78 
TCGA-G7-6796 TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-SX-A7SN TCGA-SX-A7SQ 
       34.82        25.97         6.61        84.95        19.00        41.62 
TCGA-UZ-A9PX TCGA-Y8-A897 
       27.39        18.05 

$`13Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4707 
        1.38         3.62        65.10         7.82         5.98        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4334 
       53.42         3.58        27.78        62.07        80.68        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 
       13.41        24.62        33.47        44.55        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00        79.89        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       18.15        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       56.28        55.33        56.94        55.33        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       37.15        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.28        23.31         0.76        19.63        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       49.25         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       16.77         0.46         6.58        33.83        10.09        30.58 
TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       61.02        54.90        34.19        19.00        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43         4.01        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A857 TCGA-O9-A75Z 
       27.65        20.25         0.36        12.13        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       99.78        87.22        42.94        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO 
       47.44        33.04        28.80        27.06        11.93        38.63 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.64        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.43               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             96.92             194.79 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            28.835             30.580 
[1] "0.4 - 96.9 (28.8)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "1.5"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        24        5        14        5
  13Q GAIN WILD-TYPE     424       98       176       95
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 24                424
  STAGE II                 5                 98
  STAGE III               14                176
  STAGE IV                 5                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q GAIN MUTATED    27   6  17   0
  13Q GAIN WILD-TYPE 435 117 234  15
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               27                435
  T2                6                117
  T3               17                234
  T4                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"
                    vv
clus                  N0  N1  N2
  13Q GAIN MUTATED    11   2   0
  13Q GAIN WILD-TYPE 306  41   6
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               11                306
  N1                2                 41
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V6, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    28   5
  13Q GAIN WILD-TYPE 514  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28    5
  13Q GAIN WILD-TYPE  514   84
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               28                514
  1                5                 84
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12  39
  13Q GAIN WILD-TYPE 275 533
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12   39
  13Q GAIN WILD-TYPE  275  533
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               12                275
  MALE                 39                533
[1] 2 2
[1] FALSE
D25V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  13Q GAIN MUTATED                    2                                22
  13Q GAIN WILD-TYPE                 64                               502
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  13Q GAIN MUTATED                                      27
  13Q GAIN WILD-TYPE                                   242
D25V9, multiclass
                                       clus
vv                                      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   22                502
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               27                242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, continuous
D25V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     1
  13Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           5    43
  13Q GAIN WILD-TYPE                       111   659
D25V12, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       5                111
  WHITE                                          43                659
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V13, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  36
  13Q GAIN WILD-TYPE  37 561
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   36
  13Q GAIN WILD-TYPE   37  561
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 37
  NOT HISPANIC OR LATINO               36                561
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    26  11
  14Q GAIN WILD-TYPE 606 200
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                37                806 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                11                200 
$`14Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73       137.06        98.96        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       49.97        23.47        25.91       104.52         3.55        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       11.21        42.35        80.38        87.78        86.10        77.85 
TCGA-KO-8415 TCGA-A3-3325 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 
       57.17        24.69        43.20        72.07        57.37         3.32 
TCGA-B0-4696 TCGA-B0-4699 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4770 TCGA-BP-4799 
       28.47         3.62        74.17        31.89        10.82        37.25 
TCGA-BP-4994 TCGA-CJ-4901 TCGA-CJ-6028 TCGA-CZ-4865 TCGA-CZ-5460 TCGA-BQ-5880 
       43.00        47.67        53.42         5.46        47.01        43.20 
TCGA-GL-7966 
        3.68 

$`14Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        0.99        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       16.67       103.27        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       28.04        12.13        40.70         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        2.53         3.48        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       11.31        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       62.10        73.35        67.00        53.26        60.99        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.32               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            151.96             194.79 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            47.010             29.935 
[1] "3.3 - 152.0 (47.0)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.1"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q GAIN MUTATED        12       12         8        7
  14Q GAIN WILD-TYPE     436       91       182       93
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                 12                436
  STAGE II                12                 91
  STAGE III                8                182
  STAGE IV                 7                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED    12  12  12   3
  14Q GAIN WILD-TYPE 450 111 239  12
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               12                450
  T2               12                111
  T3               12                239
  T4                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"
                    vv
clus                  N0  N1  N2
  14Q GAIN MUTATED    24   2   1
  14Q GAIN WILD-TYPE 293  41   5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               24                293
  N1                2                 41
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    24   5
  14Q GAIN WILD-TYPE 518  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     24    5
  14Q GAIN WILD-TYPE  518   84
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               24                518
  1                5                 84
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  24
  14Q GAIN WILD-TYPE 272 548
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   24
  14Q GAIN WILD-TYPE  272  548
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                272
  MALE                 24                548
[1] 2 2
[1] FALSE
D26V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  14Q GAIN MUTATED                   20                                16
  14Q GAIN WILD-TYPE                 46                               508
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  14Q GAIN MUTATED                                       3
  14Q GAIN WILD-TYPE                                   266
D26V9, multiclass
                                       clus
vv                                      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  20                 46
  KIDNEY CLEAR CELL RENAL CARCINOMA                   16                508
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                3                266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V10, continuous
D26V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     1
  14Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           2    35
  14Q GAIN WILD-TYPE                       114   667
D26V12, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          35                667
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V13, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  23
  14Q GAIN WILD-TYPE  40 574
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   23
  14Q GAIN WILD-TYPE   40  574
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 40
  NOT HISPANIC OR LATINO               23                574
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    40  11
  15Q GAIN WILD-TYPE 592 200
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                51                792 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                11                200 
$`15Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8346 
      141.73       137.06        98.96        30.25        28.11        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      151.96        49.97        23.47       104.52         3.55        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 
       11.21        42.35        74.93        16.67        80.38        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3325 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3387 
       77.85        57.17        24.69        24.16        43.20        20.28 
TCGA-AK-3430 TCGA-AK-3433 TCGA-B0-4688 TCGA-B0-5081 TCGA-B4-5838 TCGA-BP-4174 
       15.78        72.07         3.32        11.90         5.46        61.78 
TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4342 TCGA-BP-4803 TCGA-BP-4969 TCGA-BP-4994 
       54.90         0.07        74.17         6.71        58.98        43.00 
TCGA-BP-5173 TCGA-BP-5185 TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4897 TCGA-CW-5585 
        1.78        37.22        79.66        77.36        59.44        85.78 
TCGA-CW-5588 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-AL-A5DJ TCGA-B1-7332 
       66.31        61.41        56.28        47.01        49.25         7.33 
TCGA-BQ-5892 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       11.97        84.95        14.07 

$`15Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       129.37        87.91        25.48        25.91        65.19 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        0.99        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 
      100.87        76.90        10.68        79.04        92.71        87.78 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
      103.27        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 
      109.91        29.10        84.36        73.08        66.31        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        1.41         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       11.80        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       64.27        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        21.21        15.16        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       10.98        37.25        36.95        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       38.30        42.44        37.25        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       49.25        47.18        74.27        75.06        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 
        7.36        64.57        92.02        81.83         5.39        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       55.33        56.94        55.33        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       57.21        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       22.49         0.13        12.82        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            151.96             194.79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             49.97              29.90 
[1] "0.1 - 152.0 (50.0)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.5"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED        17       15        12        8
  15Q GAIN WILD-TYPE     431       88       178       92
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                 17                431
  STAGE II                15                 88
  STAGE III               12                178
  STAGE IV                 8                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED    17  15  19   1
  15Q GAIN WILD-TYPE 445 108 232  14
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               17                445
  T2               15                108
  T3               19                232
  T4                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"
                    vv
clus                  N0  N1  N2
  15Q GAIN MUTATED    25   4   1
  15Q GAIN WILD-TYPE 292  39   5
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               25                292
  N1                4                 39
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    32   7
  15Q GAIN WILD-TYPE 510  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     32    7
  15Q GAIN WILD-TYPE  510   82
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               32                510
  1                7                 82
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    19  33
  15Q GAIN WILD-TYPE 268 539
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     19   33
  15Q GAIN WILD-TYPE  268  539
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               19                268
  MALE                 33                539
[1] 2 2
[1] FALSE
D27V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  15Q GAIN MUTATED                   21                                26
  15Q GAIN WILD-TYPE                 45                               498
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  15Q GAIN MUTATED                                       5
  15Q GAIN WILD-TYPE                                   264
D27V9, multiclass
                                       clus
vv                                      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                   26                498
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                5                264
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, continuous
D27V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           4    48
  15Q GAIN WILD-TYPE                       112   654
D27V12, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       4                112
  WHITE                                          48                654
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V13, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4  31
  15Q GAIN WILD-TYPE  38 566
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   31
  15Q GAIN WILD-TYPE   38  566
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               31                566
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   213  48
  16P GAIN WILD-TYPE 419 163
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               261                582 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                48                163 
$`16P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73       137.06        98.96        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       49.97        23.47        25.48        25.91       104.52         3.55 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       11.21        42.35        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3358 
       77.85        57.17        24.16        37.15        24.69        42.97 
TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 
       24.16        18.87        20.28        72.07        57.37        45.93 
TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4833 TCGA-B0-4838 
        3.62        19.73        43.96        46.59        78.44        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5102 TCGA-B0-5106 
       53.88         6.71        43.30        11.90        90.87        52.54 
TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       11.80        37.22        14.76        48.89        56.78        60.33 
TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5838 
        1.68        32.98         0.23         1.25         0.53         5.46 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 
       25.55        25.91        29.88         4.93       101.06        93.34 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 
        0.43        89.36        61.78         0.07        93.99        31.89 
TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       11.31        12.30        13.15        68.38        11.64        15.78 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 
       10.98         6.71        47.97        71.41         6.74        58.98 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4994 
       48.89        49.38        14.93        36.07         3.88        43.00 
TCGA-BP-4995 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5198 TCGA-BP-5200 
       45.07         1.78        30.64        62.86        19.82        34.95 
TCGA-CJ-4636 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 
       63.25        11.05        79.66        74.27        77.36        69.86 
TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 
       63.98        59.44        47.67        51.29        49.28        63.88 
TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 
       72.00        84.66        22.32        61.91        62.10        53.42 
TCGA-CW-5581 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       92.02        66.31        74.66        69.21        58.75         6.77 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5467 
       61.41        23.74        56.28        55.33        47.01         2.40 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-EU-5905 
       31.10        67.96        12.16        37.15        66.02         3.91 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JJ 
        7.04        75.55        58.22       100.27        56.91        35.67 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93X 
       29.36        25.58         5.29        16.18        22.49        12.82 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 
       18.21        61.05         0.10        35.18        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-5398 
       12.99         9.63        76.64        13.55         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 
       21.67         6.58        30.58        12.46        10.16        28.18 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 
       19.23         0.16        12.30        86.76        43.20        47.80 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       26.04        25.35         7.66         0.95       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 
       96.92        50.40        11.28         7.04         3.81       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 
       35.93        24.46        40.77        51.19        61.02        19.00 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 
       51.78        25.15        17.98        17.33       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
       27.65         1.05        17.95         0.89        11.21        68.12 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S 
       11.84        56.75         5.49        16.80         2.04        85.78 
TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       22.26        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       34.29        30.38         0.36        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 
        6.61        84.95        52.27        50.60        78.90        17.75 
TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       47.90        33.04        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       41.62        26.47        48.30        60.03        14.83         0.53 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       52.11        30.67        25.68        27.39        12.99        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8S0 
       18.05        15.62         6.02 

$`16P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 
       51.06        31.33       129.37        87.91        65.19         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
      103.27        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
       47.21         0.53        39.16        49.08        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       18.44        88.37        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.64        28.31        65.52        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         1.38        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14         3.16         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       20.25        15.72         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       33.50        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        68.71        40.70        45.30 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 
       29.03         2.27        36.85        70.52        20.94        11.24 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        2.24        21.86        52.08        15.95        62.89        90.48 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        19.30        35.90        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 
       17.59         1.94        16.21        18.21        21.44        79.17 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 
      112.80       101.13        15.78        46.68        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
       35.90        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5836 TCGA-B4-5843 
       21.57        16.67         9.57         5.75         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       24.66        17.19        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
       14.27         0.53        34.39        14.30        27.29        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 
      111.02        85.51        94.72        90.28        32.61        99.85 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       21.21        15.16        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       31.33        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
       61.97        60.59        13.51        56.91        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 
       36.53        20.38        36.39        37.25        36.95         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       57.40        14.24        45.50         7.23        47.11        53.65 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       46.45        16.47         5.82        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10         6.35        79.30        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 
       23.47        13.41        24.62        33.47        44.55        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95        59.84        46.55        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
       65.69        54.61        53.52        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       49.25        47.18        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4890 
       61.91        57.83        64.18        30.64        51.52        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 
       26.93        50.01        24.66        27.65        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       56.35        49.97        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 
       38.56        45.14         3.06         4.57        18.81        79.89 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 
       25.71        18.87        25.25        18.15        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       53.26        60.99        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       64.57        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        47.08        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 
       93.04         5.46        63.42        58.82         0.82        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       47.54        22.52         1.94        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       65.88        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J2 
        2.01        19.43        19.96        15.25        10.85        59.01 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       51.52        38.99        26.43        30.71        24.33        31.20 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
        0.13        11.57        19.63        19.13         0.89         0.23 
TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
       29.46        23.28         8.28        12.46        58.45        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A47O 
       25.08        44.61        49.25         7.33        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 
        3.55        16.77         0.46        33.83        10.09        34.49 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
       50.50        26.40        20.61         6.81        14.86        17.49 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 
       19.27         8.88        63.72        22.92        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        30.28        13.25        10.88        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
        2.76        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 
       20.12         7.63         7.17        11.61        13.61        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.78         3.75        14.63         3.02        79.86        80.88 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       54.90        34.19        10.68        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
       34.82        13.68        25.84         6.38        16.90        80.65 
TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X 
       12.92        12.43         4.60        13.41        73.25        19.99 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A561 
       88.24        67.17        21.34         0.13        27.78        27.65 
TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5ED 
       20.25        12.13        25.97        21.44        15.48        92.58 
TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SO 
       16.01        12.85        14.07        47.44        11.93        38.63 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-WN-A9G9 
       43.76        18.02        21.93        86.27        38.86        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       29.00        18.64        18.64        25.28         6.74        13.28 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            194.79             129.37 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             27.06              31.33 
[1] "0.1 - 194.8 (27.1)" "0.1 - 129.4 (31.3)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED       143       29        61       26
  16P GAIN WILD-TYPE     305       74       129       74
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                143                305
  STAGE II                29                 74
  STAGE III               61                129
  STAGE IV                26                 74
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P GAIN MUTATED   149  36  75   5
  16P GAIN WILD-TYPE 313  87 176  10
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              149                313
  T2               36                 87
  T3               75                176
  T4                5                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  16P GAIN MUTATED    89  12   3
  16P GAIN WILD-TYPE 228  31   3
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               89                228
  N1               12                 31
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   142  22
  16P GAIN WILD-TYPE 400  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    142   22
  16P GAIN WILD-TYPE  400   67
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              142                400
  1               22                 67
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    72 198
  16P GAIN WILD-TYPE 215 374
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     72  198
  16P GAIN WILD-TYPE  215  374
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               72                215
  MALE                198                374
[1] 2 2
[1] FALSE
D28V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16P GAIN MUTATED                   21                               106
  16P GAIN WILD-TYPE                 45                               418
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16P GAIN MUTATED                                     143
  16P GAIN WILD-TYPE                                   126
D28V9, multiclass
                                       clus
vv                                      16P GAIN MUTATED 16P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  106                418
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              143                126
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V10, continuous
D28V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     5
  16P GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          27   229
  16P GAIN WILD-TYPE                        89   473
D28V12, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           5                 10
  BLACK OR AFRICAN AMERICAN                      27                 89
  WHITE                                         229                473
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V13, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    12 194
  16P GAIN WILD-TYPE  30 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12  194
  16P GAIN WILD-TYPE   30  403
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 30
  NOT HISPANIC OR LATINO              194                403
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   207  42
  16Q GAIN WILD-TYPE 425 169
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               249                594 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                42                169 
$`16Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73       137.06        98.96        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       49.97        23.47        25.48        25.91       104.52         3.55 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       11.21        42.35        74.93        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3382 
       77.85        57.17        24.16        24.69        42.97        18.87 
TCGA-A3-3387 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4707 
       20.28        72.07        57.37        45.93         3.62        19.73 
TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-5077 
       43.96        46.59        78.44        27.42        53.88        43.30 
TCGA-B0-5081 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 
       11.90        90.87        52.54        11.80        37.22        48.89 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5838 
       56.78        60.33         1.68         0.23         1.25         5.46 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 
       25.55        25.91        29.88         4.93       101.06        93.34 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 
        0.43        89.36        61.78         0.07        93.99        31.89 
TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       11.31        12.30        13.15        68.38        11.64        15.78 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 
       10.98         6.71        47.97        71.41         6.74        58.98 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4994 
       48.89        49.38        14.93        36.07         3.88        43.00 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4636 
        1.78        30.64        62.86        19.82        34.95        63.25 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 
       11.05        79.66        74.27        77.36        69.86        63.98 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 
       59.44        47.67        51.29        49.28        63.88        72.00 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 
       84.66        22.32        61.91        62.10        53.42        92.02 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4866 
       66.31        74.66        69.21        58.75         6.77        61.41 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5984 
       56.28        55.33        47.01         2.40        31.10        67.96 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J1 
       12.16        37.15        66.02         3.91         7.04        75.55 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JJ TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       58.22       100.27        56.91        35.67        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 
        5.29        16.18        22.49        12.82        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        0.10        35.18        16.64        30.48        25.64        23.97 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 
       16.96         8.48        16.31        15.75        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-8121 
        2.20        19.56        21.67         6.58        30.58        12.46 
TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       10.16        28.18         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 
       22.06         2.10        19.23         0.16        12.30        86.76 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 
       43.20        47.80        26.04        25.35         0.95       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7834 
       48.26        96.92        50.40         7.04         3.81       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5902 
       35.93        24.46        40.77        51.19        61.02        19.00 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 
       51.78        25.15        17.98        17.33       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
       27.65         1.05        17.95         0.89        11.21        68.12 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       11.84         5.49        16.80        19.99         2.04        85.78 
TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       22.26        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       34.29        30.38         0.36        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 
        6.61        84.95        52.27        50.60        78.90        17.75 
TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       47.90        33.04        28.80        27.06        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       41.62        26.47        48.30        60.03        14.83         0.53 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       52.11        30.67        25.68        27.39        12.99        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8S0 
       18.05        15.62         6.02 

$`16Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 
       51.06        31.33       129.37        87.91        65.19         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87        76.90        10.68        79.04        92.71        16.67 
TCGA-KO-8411 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
      103.27        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       47.21         0.53        39.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       29.92        18.44        88.37        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ 
       55.76        20.71        18.64        28.31        65.52        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61        67.20        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        1.38        65.10         7.82         5.98         2.14         3.16 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        6.64         3.25        20.25        15.72         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 
       36.53        14.93        54.48        29.10        10.09        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       40.70        45.30         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       70.52        20.94        11.24         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       15.95        62.89        90.48        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       35.90        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 
       18.21        21.44        14.76        79.17       112.80       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        46.68        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 
       89.49        61.32        97.41        32.61        35.90        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
       16.67         9.57         5.75         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       24.66        17.19        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
       14.27         0.53        34.39        14.30        27.29        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4165 
      111.02        85.51        94.72        90.28        32.61        99.85 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
       21.21        15.16        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 
       54.77        49.08        44.94        12.23        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       31.33        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
       61.97        60.59        13.51        56.91        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4807 
       36.53        20.38        36.39        37.25        36.95         6.94 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       57.40        14.24        45.50         7.23        47.11        53.65 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
       52.27         9.63        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27         0.95        59.84        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
       75.88        65.69        54.61        53.52        58.95        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       83.97        49.25        47.18        75.06        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        61.91        57.83        64.18        30.64        51.52 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       50.24        56.35        49.97        58.92        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5684 
       79.89        25.71        18.87        25.25        18.15        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        60.99        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
        7.36        64.57        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4862 
       25.45        46.16         0.59        47.08        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       23.74        18.44        56.94        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        57.21        47.54        22.52         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        65.88        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       23.90        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       10.85        59.01         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.81        54.64        51.52        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7732 
       24.33        31.20         0.13        11.57        19.63        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
        0.89         0.23        29.46        23.28         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46         9.63        58.45        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       49.25         7.33        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 
        0.46        33.83        10.09        34.49        50.50        26.40 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 
       20.61         6.81        14.86        17.49        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        22.92        21.63        40.83        26.04        30.28 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       13.25        10.88         7.66        11.97         7.92         2.76 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       93.34        44.84        61.28        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 
       11.28         7.63         7.17        11.61        13.61        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
       13.78         3.75        14.63         3.02        79.86        80.88 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
       54.90        34.19        10.68        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
       34.82        13.68        25.84         6.38        16.90        80.65 
TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
       12.92        12.43         4.60        13.41        56.75        73.25 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A561 
       88.24        67.17        21.34         0.13        27.78        27.65 
TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5ED 
       20.25        12.13        25.97        21.44        15.48        92.58 
TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SO 
       16.01        12.85        14.07        47.44        11.93        38.63 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-WN-A9G9 
       43.76        18.02        21.93        86.27        38.86        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       29.00        18.64        18.64        25.28         6.74        13.28 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            194.79             129.37 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             27.42              31.30 
[1] "0.1 - 194.8 (27.4)" "0.1 - 129.4 (31.3)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED       141       29        57       21
  16Q GAIN WILD-TYPE     307       74       133       79
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                141                307
  STAGE II                29                 74
  STAGE III               57                133
  STAGE IV                21                 79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q GAIN MUTATED   145  34  70   4
  16Q GAIN WILD-TYPE 317  89 181  11
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1              145                317
  T2               34                 89
  T3               70                181
  T4                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"
                    vv
clus                  N0  N1  N2
  16Q GAIN MUTATED    85  10   2
  16Q GAIN WILD-TYPE 232  33   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               85                232
  N1               10                 33
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   134  18
  16Q GAIN WILD-TYPE 408  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    134   18
  16Q GAIN WILD-TYPE  408   71
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0              134                408
  1               18                 71
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    72 186
  16Q GAIN WILD-TYPE 215 386
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     72  186
  16Q GAIN WILD-TYPE  215  386
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               72                215
  MALE                186                386
[1] 2 2
[1] FALSE
D29V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16Q GAIN MUTATED                   21                                98
  16Q GAIN WILD-TYPE                 45                               426
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16Q GAIN MUTATED                                     139
  16Q GAIN WILD-TYPE                                   130
D29V9, multiclass
                                       clus
vv                                      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                   98                426
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              139                130
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, continuous
D29V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     5
  16Q GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          28   217
  16Q GAIN WILD-TYPE                        88   485
D29V12, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           5                 10
  BLACK OR AFRICAN AMERICAN                      28                 88
  WHITE                                         217                485
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V13, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12 185
  16Q GAIN WILD-TYPE  30 412
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12  185
  16Q GAIN WILD-TYPE   30  412
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 30
  NOT HISPANIC OR LATINO              185                412
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED   156  21
  17P GAIN WILD-TYPE 476 190
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               177                666 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                21                190 
$`17P GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4696 TCGA-B0-5102 
       24.16        24.69        10.49        45.93        28.47        90.87 
TCGA-B0-5109 TCGA-B4-5838 TCGA-B8-4621 TCGA-B8-5551 TCGA-BP-4177 TCGA-BP-4756 
       19.30         5.46        25.91         0.53        54.90        12.30 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5185 TCGA-BP-5200 
       13.15        68.38        31.30         1.78        37.22        34.95 
TCGA-CJ-4873 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4866 TCGA-CZ-5469 TCGA-EU-5905 
       74.27        47.67        49.28        61.41        31.10         3.91 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JQ 
        4.57        34.85        56.81        30.71        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-A4-7286 TCGA-A4-7288 
        5.29        16.18        22.49         0.13        18.21        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
       19.13         0.89        16.64        25.64        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU 
        0.76        19.63        19.73        14.33        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       15.75         8.28        12.46        76.64        13.55        30.35 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       49.25         2.20         7.33        21.67        24.56         3.55 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        6.58        33.83        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 
       22.06        19.23         0.16        17.49        47.80        25.35 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 
        0.95        11.97         7.92        48.26        96.92        50.40 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
       40.77        51.19        61.02        34.19        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 
        2.40         1.18         4.01        51.78        39.25        34.82 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
      194.79         3.68         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       11.21        68.12        13.41        11.84        56.75         5.49 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       16.80         2.04        88.24        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
       27.78        30.38        27.65        20.25        15.48        87.22 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        6.61        84.95        17.75        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       28.80        19.00        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       43.76        60.03        14.83         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 
       30.67        25.68        27.39        12.99        29.00        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.62        25.28         6.02 

$`17P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       86.10        77.85        57.17        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 
       12.16        36.82        47.21         0.53        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       82.32        51.25        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.55        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        64.27        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       12.33        33.99        31.33        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 
       13.41        24.62        33.47        19.82        44.55        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 
       21.24        83.97        49.25        79.66        47.18        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        56.35        49.97        51.29        58.92        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       57.21        47.54        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J8 
        2.01        19.43        19.96        15.25        10.85        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       75.42        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7583 
       24.33        31.20        12.82        11.57        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A48D 
       35.18         0.23        30.48        29.46        23.28        12.46 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 
        8.48        12.99         9.63        58.45        25.08        44.61 
TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 
       19.56        16.87        16.77         0.46        10.09        34.49 
TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.61         2.10         6.81        14.86        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 
       19.27         8.88        63.72        22.92        43.20        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.66         2.76       123.62        93.34        44.84        61.28 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
       49.84        26.27        20.12        11.28         7.63         7.17 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G 
       79.86        80.88        54.90        19.00        10.68         0.43 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 
       48.62        11.05        25.15        13.68        12.92        27.65 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83W TCGA-MH-A854 
        4.60        73.25        19.99        85.78        67.17         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5ED 
       12.13        25.97        21.44        99.78        42.94        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
       52.27        16.01        50.60        78.90        12.85        14.07 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       27.06        11.93        38.63        18.02        21.93        86.27 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       26.01        18.64        18.64        18.05         6.74        13.28 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.13               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            194.79             151.96 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            22.060             35.985 
[1] "0.1 - 194.8 (22.1)" "0.1 - 152.0 (36.0)"
[1] "hr=" "1.7"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED       130       18        24        6
  17P GAIN WILD-TYPE     318       85       166       94
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                130                318
  STAGE II                18                 85
  STAGE III               24                166
  STAGE IV                 6                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED   133  24  27   2
  17P GAIN WILD-TYPE 329  99 224  13
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1              133                329
  T2               24                 99
  T3               27                224
  T4                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17P GAIN MUTATED    32  11   1
  17P GAIN WILD-TYPE 285  32   5
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               32                285
  N1               11                 32
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    67   3
  17P GAIN WILD-TYPE 475  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     67    3
  17P GAIN WILD-TYPE  475   86
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               67                475
  1                3                 86
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    43 144
  17P GAIN WILD-TYPE 244 428
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     43  144
  17P GAIN WILD-TYPE  244  428
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               43                244
  MALE                144                428
[1] 2 2
[1] FALSE
D30V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17P GAIN MUTATED                    0                                24
  17P GAIN WILD-TYPE                 66                               500
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17P GAIN MUTATED                                     163
  17P GAIN WILD-TYPE                                   106
D30V9, multiclass
                                       clus
vv                                      17P GAIN MUTATED 17P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   24                500
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              163                106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V10, continuous
D30V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  2     6
  17P GAIN WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          31   140
  17P GAIN WILD-TYPE                        85   562
D30V12, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           6                  9
  BLACK OR AFRICAN AMERICAN                      31                 85
  WHITE                                         140                562
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V13, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4 158
  17P GAIN WILD-TYPE  38 439
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4  158
  17P GAIN WILD-TYPE   38  439
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO              158                439
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   172  28
  17Q GAIN WILD-TYPE 460 183
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               200                643 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                28                183 
$`17Q GAIN MUTATED`
TCGA-A3-3313 TCGA-A3-3325 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4707 TCGA-B0-5102 
       24.16        24.69        10.49        45.93        19.73        90.87 
TCGA-B0-5109 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4621 TCGA-B8-5551 
       19.30         0.53         5.46        23.31        25.91         0.53 
TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4768 TCGA-BP-4781 
       54.90         0.07        12.30        72.59        13.15        68.38 
TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5182 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4873 
       31.30         1.78        38.30        37.22        34.95        74.27 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4866 TCGA-CZ-5469 TCGA-EU-5905 TCGA-G6-A8L7 
       47.67        49.28        61.41        31.10         3.91        70.13 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP 
        4.57        34.85        56.81        51.52        30.71        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-A4-7286 
       25.58         5.29        16.18        22.49         0.13        18.21 
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 
       61.05        19.13         0.89         0.23        16.64        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-A5DJ TCGA-AT-A5NU 
        9.63        76.64        13.55        30.35        49.25         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        6.58        33.83        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 
       22.06         2.10        19.23         0.16        17.49        86.76 
TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
       47.80        26.04        25.35        13.25         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7053 
       11.97         7.92        48.26        96.92        50.40        49.84 
TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       11.28         7.04         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-EV-5901 
        3.02        40.77        80.88        51.19        61.02        34.19 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
       24.89        13.08         2.40         1.18         4.01        51.78 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        39.25        34.82        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
       17.33        16.90        80.65       194.79         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH 
       12.43        17.95         0.89        11.21        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83T 
       11.84        56.75         5.49        16.80         2.04        88.24 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-AAVL 
       20.25        15.48        87.22         6.61        84.95        16.01 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       60.03        14.83         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A898 
       25.68        27.39        12.99        29.00        15.91        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$`17Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       86.10        77.85        57.17        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 
       12.16        36.82        47.21         0.53        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       82.32        51.25        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        1.25         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       27.55        25.05        24.66        17.19        25.55        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60         6.38        14.27        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       64.27        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        21.21        15.16        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       28.87        48.10         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 
       52.27         9.63        62.86        74.40        49.15        42.44 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.25        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        56.35        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
       18.12         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J8 
        2.01        19.43        19.96        15.25        10.85        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JN 
       75.42        54.64        35.67        38.99        26.43        24.33 
TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       31.20        12.82        11.57        19.63         0.10        35.18 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A48D TCGA-A4-A5Y1 TCGA-AL-3467 
       30.48        29.46        23.28        12.46        12.99        58.45 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 
       25.08        44.61        19.56         0.46        10.09        34.49 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
       20.61         6.81        14.86        12.30        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 
       30.28        10.88         2.76       123.62        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 
       61.28        26.27        20.12         7.63         7.17        79.86 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 
       54.90        19.00        10.68         0.43        48.62        25.15 
TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X 
       13.68        12.92        27.65         4.60        73.25        19.99 
TCGA-IA-A83S TCGA-IA-A83W TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       85.78        67.17         0.36        12.13        25.97        21.44 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       99.78        42.94        92.58        52.27        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PN 
       12.85        27.06        11.93        38.63        18.02        21.93 
TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ 
       86.27        26.01        18.64        18.64        18.05         6.74 
TCGA-Y8-A8S1 
       13.28 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            194.79             151.96 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             19.99              36.53 
[1] "0.1 - 194.8 (20.0)" "0.1 - 152.0 (36.5)"
[1] "hr=" "1.4"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED       138       19        33       10
  17Q GAIN WILD-TYPE     310       84       157       90
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                138                310
  STAGE II                19                 84
  STAGE III               33                157
  STAGE IV                10                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q GAIN MUTATED   141  26  39   2
  17Q GAIN WILD-TYPE 321  97 212  13
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1              141                321
  T2               26                 97
  T3               39                212
  T4                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  17Q GAIN MUTATED    42  12   3
  17Q GAIN WILD-TYPE 275  31   3
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               42                275
  N1               12                 31
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V6, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    78   6
  17Q GAIN WILD-TYPE 464  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     78    6
  17Q GAIN WILD-TYPE  464   83
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               78                464
  1                6                 83
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    55 155
  17Q GAIN WILD-TYPE 232 417
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     55  155
  17Q GAIN WILD-TYPE  232  417
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               55                232
  MALE                155                417
[1] 2 2
[1] FALSE
D31V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17Q GAIN MUTATED                    0                                30
  17Q GAIN WILD-TYPE                 66                               494
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17Q GAIN MUTATED                                     180
  17Q GAIN WILD-TYPE                                    89
D31V9, multiclass
                                       clus
vv                                      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   30                494
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              180                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V10, continuous
D31V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  2     6
  17Q GAIN WILD-TYPE                                0     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          36   157
  17Q GAIN WILD-TYPE                        80   545
D31V12, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           6                  9
  BLACK OR AFRICAN AMERICAN                      36                 80
  WHITE                                         157                545
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V13, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 173
  17Q GAIN WILD-TYPE  36 424
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  173
  17Q GAIN WILD-TYPE   36  424
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 36
  NOT HISPANIC OR LATINO              173                424
[1] 2 2
[1] FALSE

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                  0   1
  18P GAIN MUTATED    47   7
  18P GAIN WILD-TYPE 585 204
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                789 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                204 
$`18P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 
      141.73       137.06        62.37       151.96        31.33        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8436 
       25.48        25.91       104.52         3.55        52.27        42.35 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8415 TCGA-A3-3308 
       10.68        74.93        80.38        87.78        57.17         0.53 
TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4710 TCGA-B0-5113 
       24.69        43.20        18.87        72.07         3.16        11.80 
TCGA-B0-5693 TCGA-B2-5633 TCGA-B4-5838 TCGA-BP-4177 TCGA-BP-4342 TCGA-BP-4351 
      101.13        11.77         5.46        54.90        74.17        31.89 
TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 TCGA-CJ-4872 TCGA-CJ-4897 
       13.15        48.95        16.47        46.55        47.18        59.44 
TCGA-CJ-4905 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 TCGA-CZ-5467 
       49.18        64.57        81.83        85.78        55.33         2.40 
TCGA-2Z-A9J1 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 
       75.55        12.99         9.63        30.58        34.49        15.12 
TCGA-DW-5560 TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-HE-A5NJ TCGA-SX-A7SS 
       11.61        51.78        17.98        17.33        56.75        48.30 

$`18P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       71.41        28.80        54.74        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
       47.24        49.97       123.12        51.06       129.37        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19         0.99        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
       59.08       115.00       100.87        76.90        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.27        86.10        77.85        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 TCGA-A3-3313 
       12.66        12.16        36.82        47.21        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       19.73        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        29.95        19.30        35.90        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5694 
       37.22        14.76        79.17       112.80        48.89        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
        1.68        12.30        21.30        31.30        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        0.53         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        60.95        15.78        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 
       36.95        27.22         3.88        46.45         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       44.55        34.95        31.27         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 
       53.42        75.58        62.66        83.77         7.36        92.02 
TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        56.28        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 
        0.46         6.58        33.83        10.09        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.17         3.81        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68        25.84         6.38        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       11.84        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       16.31        41.62        26.47        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.53               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            151.96             194.79 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            44.875             29.950 
[1] "0.5 - 152.0 (44.9)" "0.1 - 194.8 (29.9)"
[1] "hr=" "2.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED        26       10        11        6
  18P GAIN WILD-TYPE     422       93       179       94
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                 26                422
  STAGE II                10                 93
  STAGE III               11                179
  STAGE IV                 6                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED    28  11  14   1
  18P GAIN WILD-TYPE 434 112 237  14
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               28                434
  T2               11                112
  T3               14                237
  T4                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"
                    vv
clus                  N0  N1  N2
  18P GAIN MUTATED    26   3   0
  18P GAIN WILD-TYPE 291  40   6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               26                291
  N1                3                 40
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    35   4
  18P GAIN WILD-TYPE 507  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     35    4
  18P GAIN WILD-TYPE  507   85
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               35                507
  1                4                 85
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    20  34
  18P GAIN WILD-TYPE 267 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     20   34
  18P GAIN WILD-TYPE  267  538
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               20                267
  MALE                 34                538
[1] 2 2
[1] FALSE
D32V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18P GAIN MUTATED                   17                                25
  18P GAIN WILD-TYPE                 49                               499
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18P GAIN MUTATED                                      12
  18P GAIN WILD-TYPE                                   257
D32V9, multiclass
                                       clus
vv                                      18P GAIN MUTATED 18P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  17                 49
  KIDNEY CLEAR CELL RENAL CARCINOMA                   25                499
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               12                257
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V10, continuous
D32V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           2    51
  18P GAIN WILD-TYPE                       114   651
D32V12, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          51                651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V13, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4  35
  18P GAIN WILD-TYPE  38 562
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   35
  18P GAIN WILD-TYPE   38  562
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               35                562
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    45   5
  18Q GAIN WILD-TYPE 587 206
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                50                793 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                206 
$`18Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 
      141.73       137.06        62.37       151.96        31.33        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8436 
       25.48        25.91       104.52         3.55        52.27        42.35 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8415 TCGA-A3-3308 TCGA-A3-3325 
       74.93        80.38        87.78        57.17         0.53        24.69 
TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-5113 
       43.20        18.87        72.07        19.73         3.16        11.80 
TCGA-B0-5693 TCGA-B2-5633 TCGA-B4-5838 TCGA-BP-4177 TCGA-BP-4342 TCGA-BP-4351 
      101.13        11.77         5.46        54.90        74.17        31.89 
TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 TCGA-CJ-4897 TCGA-CJ-4905 
       13.15        48.95        16.47        46.55        59.44        49.18 
TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 TCGA-CZ-5467 TCGA-2Z-A9J1 
       64.57        81.83        85.78        55.33         2.40        75.55 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-5155 TCGA-DW-5560 TCGA-G7-6790 TCGA-G7-A8LB 
       30.58        34.49        15.12        11.61        51.78        17.98 
TCGA-G7-A8LC TCGA-SX-A7SS 
       17.33        48.30 

$`18Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       71.41        28.80        54.74        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
       47.24        49.97       123.12        51.06       129.37        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
       65.19         0.99        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
       59.08       115.00       100.87        76.90        10.68        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
       92.71        16.67       103.27        86.10        77.85        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3311 
       63.95        12.66        12.16        36.82        47.21        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       36.36        38.99        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        29.95        19.30        35.90        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5694 
       37.22        14.76        79.17       112.80        48.89        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
        1.68        12.30        21.30        31.30        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        0.53         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        64.27        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4795 
       68.38        11.64        60.95        15.78        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 
       36.95        27.22         3.88        46.45         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       44.55        34.95        31.27         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        58.92        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5581 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02         5.39        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       57.21        47.54        22.52         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       10.09        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
       20.61         0.46         1.15        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 
       11.28         7.63         7.04         7.17         3.81        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       13.08         2.40         1.18         0.43         4.01        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        6.38        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.53               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            151.96             194.79 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            44.875             29.950 
[1] "0.5 - 152.0 (44.9)" "0.1 - 194.8 (29.9)"
[1] "hr=" "3.2"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED        25       10        11        4
  18Q GAIN WILD-TYPE     423       93       179       96
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                 25                423
  STAGE II                10                 93
  STAGE III               11                179
  STAGE IV                 4                 96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED    25  11  14   0
  18Q GAIN WILD-TYPE 437 112 237  15
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               25                437
  T2               11                112
  T3               14                237
  T4                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"
                    vv
clus                  N0  N1  N2
  18Q GAIN MUTATED    25   1   0
  18Q GAIN WILD-TYPE 292  42   6
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               25                292
  N1                1                 42
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V6, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    34   3
  18Q GAIN WILD-TYPE 508  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     34    3
  18Q GAIN WILD-TYPE  508   86
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               34                508
  1                3                 86
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20  30
  18Q GAIN WILD-TYPE 267 542
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20   30
  18Q GAIN WILD-TYPE  267  542
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               20                267
  MALE                 30                542
[1] 2 2
[1] FALSE
D33V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18Q GAIN MUTATED                   16                                25
  18Q GAIN WILD-TYPE                 50                               499
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18Q GAIN MUTATED                                       9
  18Q GAIN WILD-TYPE                                   260
D33V9, multiclass
                                       clus
vv                                      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  16                 50
  KIDNEY CLEAR CELL RENAL CARCINOMA                   25                499
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                9                260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V10, continuous
D33V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           2    48
  18Q GAIN WILD-TYPE                       114   654
D33V12, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          48                654
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V13, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4  32
  18Q GAIN WILD-TYPE  38 565
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   32
  18Q GAIN WILD-TYPE   38  565
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               32                565
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    51  23
  19P GAIN WILD-TYPE 581 188
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                74                769 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                23                188 
$`19P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      141.73        30.25        28.11        24.79        62.37       151.96 
TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       49.97        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8414 
       11.21        42.35        16.67        80.38        87.78        77.85 
TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 
       24.69        43.20        18.87        72.07        57.37        45.93 
TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4822 
        3.32         3.62         3.16        46.59        40.44        36.53 
TCGA-B0-4844 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5832 
       10.29         7.30        10.95        90.87        19.30         0.23 
TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4166 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4352 
        5.46        23.31         0.43        74.17        31.89        11.31 
TCGA-BP-4768 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5178 TCGA-BP-5185 
       13.15         6.74        58.98        43.00        62.86        37.22 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4897 
       19.82        34.95        46.55        79.66        74.27        59.44 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CW-5591 
       49.28        63.88        84.66        61.91        53.42        74.66 
TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
       46.16        61.41        56.28        55.33        47.01        10.85 
TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 TCGA-BQ-5885 TCGA-BQ-5892 
       57.21        31.10        67.96         3.91        30.28        11.97 
TCGA-G7-A8LC TCGA-GL-7966 
       17.33         3.68 

$`19P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.56        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 
       54.74        23.28        44.91        28.80        47.24       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       65.19        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
      103.27        86.10        57.17        61.58        63.95        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       49.08        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       38.99        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        5.98         2.14        19.73        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       20.25        15.72         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        11.64        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        29.95        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         1.25         0.53         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 
       62.86        54.77        49.08        44.94        12.23        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22        61.51        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        44.55        31.27         0.95        59.84 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        3.06         4.57        18.81        72.00        79.89        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        25.25        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        60.99        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        66.31        78.18         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       56.94        55.33        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40         1.94        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.02        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       22.49         0.13        12.82        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.23               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            151.96             194.79 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            41.395             29.880 
[1] "0.2 - 152.0 (41.4)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED        21       15        19       20
  19P GAIN WILD-TYPE     427       88       171       80
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                 21                427
  STAGE II                15                 88
  STAGE III               19                171
  STAGE IV                20                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    22  15  35   3
  19P GAIN WILD-TYPE 440 108 216  12
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               22                440
  T2               15                108
  T3               35                216
  T4                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"
                    vv
clus                  N0  N1  N2
  19P GAIN MUTATED    35   7   2
  19P GAIN WILD-TYPE 282  36   4
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               35                282
  N1                7                 36
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V6, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    46  17
  19P GAIN WILD-TYPE 496  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     46   17
  19P GAIN WILD-TYPE  496   72
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               46                496
  1               17                 72
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    22  53
  19P GAIN WILD-TYPE 265 519
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22   53
  19P GAIN WILD-TYPE  265  519
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               22                265
  MALE                 53                519
[1] 2 2
[1] FALSE
D34V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19P GAIN MUTATED                   19                                52
  19P GAIN WILD-TYPE                 47                               472
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19P GAIN MUTATED                                       4
  19P GAIN WILD-TYPE                                   265
D34V9, multiclass
                                       clus
vv                                      19P GAIN MUTATED 19P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  19                 47
  KIDNEY CLEAR CELL RENAL CARCINOMA                   52                472
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                4                265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V10, continuous
D34V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     2
  19P GAIN WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           1    72
  19P GAIN WILD-TYPE                       115   630
D34V12, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       1                115
  WHITE                                          72                630
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V13, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  49
  19P GAIN WILD-TYPE  39 548
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   49
  19P GAIN WILD-TYPE   39  548
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               49                548
[1] 2 2
[1] FALSE

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                  0   1
  19Q GAIN MUTATED    52  25
  19Q GAIN WILD-TYPE 580 186
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                77                766 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                186 
$`19Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8336 TCGA-KL-8339 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      141.73        30.25        28.11        62.37       151.96        49.97 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 
       25.91       104.52         3.55        52.27        11.21        42.35 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8414 TCGA-A3-3325 TCGA-A3-3336 
       16.67        80.38        87.78        77.85        24.69        34.29 
TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 
       43.20        18.87        72.07        67.20        57.37        45.93 
TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4821 
        3.32         3.62        19.73         3.16        46.59        40.44 
TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5102 
       36.53        10.09        10.29         7.30        10.95        90.87 
TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4166 TCGA-BP-4342 
       19.30         0.23         5.46        23.31         0.43        74.17 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4985 
       31.89        11.31        13.15         6.74        58.98        31.30 
TCGA-BP-4994 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 
       43.00        62.86        37.22        19.82        34.95        46.55 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 
       79.66        74.27        59.44        49.28        63.88        84.66 
TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5456 
       61.91        53.42        74.66        46.16        61.41        56.28 
TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5984 
       55.33        47.01        10.85        57.21        31.10        67.96 
TCGA-EU-5905 TCGA-BQ-5885 TCGA-BQ-5892 TCGA-G7-A8LC TCGA-GL-7966 
        3.91        30.28        11.97        17.33         3.68 

$`19Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       28.80        54.74        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         0.99        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 
       79.04        92.71       103.27        86.10        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       39.16        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        21.86 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
       84.36        73.08        66.31        15.78        60.92        68.61 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       15.72         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       16.77         6.02        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        11.64        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.90        25.32        18.51        15.09         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         5.75         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       61.51        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       30.64        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       42.44        37.25        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       31.27         0.95        59.84        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        47.18        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       47.67        49.97        51.29        58.92        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00        79.89        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.15        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
        0.82        23.74        18.44        56.94        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        47.54        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       80.19        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 
       66.28        56.84        23.90        66.02        18.12         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        15.25        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        25.35        13.25        10.88         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       13.68        25.84         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.23               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            151.96             194.79 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             40.44              29.41 
[1] "0.2 - 152.0 (40.4)" "0.1 - 194.8 (29.4)"
[1] "hr=" "1.2"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED        22       15        21       20
  19Q GAIN WILD-TYPE     426       88       169       80
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                 22                426
  STAGE II                15                 88
  STAGE III               21                169
  STAGE IV                20                 80
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    23  17  36   2
  19Q GAIN WILD-TYPE 439 106 215  13
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               23                439
  T2               17                106
  T3               36                215
  T4                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  19Q GAIN MUTATED    37   6   1
  19Q GAIN WILD-TYPE 280  37   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               37                280
  N1                6                 37
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    48  19
  19Q GAIN WILD-TYPE 494  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     48   19
  19Q GAIN WILD-TYPE  494   70
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               48                494
  1               19                 70
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    23  55
  19Q GAIN WILD-TYPE 264 517
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     23   55
  19Q GAIN WILD-TYPE  264  517
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               23                264
  MALE                 55                517
[1] 2 2
[1] FALSE
D35V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19Q GAIN MUTATED                   17                                57
  19Q GAIN WILD-TYPE                 49                               467
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19Q GAIN MUTATED                                       4
  19Q GAIN WILD-TYPE                                   265
D35V9, multiclass
                                       clus
vv                                      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  17                 49
  KIDNEY CLEAR CELL RENAL CARCINOMA                   57                467
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                4                265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V10, continuous
D35V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           1    76
  19Q GAIN WILD-TYPE                       115   626
D35V12, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       1                115
  WHITE                                          76                626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V13, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  53
  19Q GAIN WILD-TYPE  39 544
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   53
  19Q GAIN WILD-TYPE   39  544
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               53                544
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   163  54
  20P GAIN WILD-TYPE 469 157
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               217                626 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                54                157 
$`20P GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
      151.96        49.97        25.91       104.52         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
       11.21        42.35        10.68        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
       86.10        77.85        12.66         0.53        24.16        49.08 
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 
       37.15        24.69        42.97        24.16        43.20        18.87 
TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 
       65.52        84.36        66.31        72.07        57.37        42.08 
TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
       45.93         3.32         1.41         1.38         3.62        65.10 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4822 
       19.73        43.96        46.59        52.21         6.02        36.53 
TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5106 
       10.09        40.70        10.29        29.03        10.95        52.54 
TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 
       19.30        11.80        21.60         0.23         5.46        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I 
       25.91        23.01        20.91        27.02         0.53         4.93 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4342 
        0.43        89.36        64.27         0.07        93.99        74.17 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 
       62.86        31.89         5.98        13.15        68.38        15.78 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 
       10.98        37.25         6.71        47.97        71.41         6.74 
TCGA-BP-4969 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5009 
       58.98        46.45        31.30        16.47        43.00        36.23 
TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5185 TCGA-BP-5191 
       28.87         1.78        30.64        62.86        37.22        31.79 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 
       19.82        34.95        46.55        11.05        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 
       74.27        77.36        66.21        61.91        59.44        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 
       49.97        51.29        49.28        63.88        84.66        22.32 
TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4854 TCGA-CZ-4857 
       61.91        66.31        74.66         1.35        46.16        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 
       69.21         6.77        14.66        61.41        56.28        47.01 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
       10.85        57.21         1.94        31.10        67.96         3.91 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-2Z-A9JS 
        7.04        75.55         4.57        54.64        30.71        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7734 
       22.49         0.13        12.82        18.21        19.13         0.89 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 
       16.64        30.48        25.64        23.97        19.63        19.73 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3468 TCGA-AL-3471 
       16.31        15.75        12.99         9.63        76.64        13.55 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 
        2.20         7.33        24.56         3.55        33.83        30.58 
TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH 
       12.46         0.46         1.15        22.06         0.16        17.49 
TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
       21.63        25.35         0.95        11.97         2.76        96.92 
TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
       50.40         3.81        11.61        13.61        35.93        14.63 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 
       80.88        51.19        19.00        13.08         2.40         4.01 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NF 
       39.25        25.15        17.98        17.33         3.68        68.12 
TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W 
       11.84         2.04        22.26        11.97        29.10        34.29 
TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       20.25         0.36         6.61        52.27        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS 
       47.90        28.80        27.06        16.31        41.62        48.30 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 
        0.53        52.11        25.68        12.99        29.00        15.91 
TCGA-Y8-A8S0 
        6.02 

$`20P GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       31.33       129.37        23.47        87.91        25.48        65.19 
TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        3.55        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
      100.87        76.90        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       39.16        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 
       52.93        45.53        29.92        18.44        88.37        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ 
       55.76        20.71        18.64        28.31        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       29.10        73.08        15.78        60.92        68.61        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        48.36        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
       40.70         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00         7.82         5.98         2.14         3.16         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        20.25        15.72         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77        40.44        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
       56.68        11.64        65.29        39.45        26.07         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        18.51        15.09         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       30.48        29.95        35.90        26.20        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67         9.57         5.75         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
       25.05        24.66        17.19        23.74         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        17.16        16.60         6.38        14.27        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        61.78        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
       21.21        15.16        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       60.59        13.51        56.91        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 
       36.53        20.38        36.39        36.95         6.94        87.45 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 
       63.62        58.68        60.30        61.22        61.51        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
       53.65        14.93        36.07        33.34        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22         3.88        46.45         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       35.21        48.10         6.35        79.30        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       22.78        13.35        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        44.55        31.27         0.95        59.84 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 
       53.52        58.95        21.24        83.97        49.25        75.06 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       64.27        71.87        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-4905 
       27.65        39.45        50.24        56.35        58.92        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       18.81        72.00        79.89        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.15        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
      105.93        83.90       103.43        18.77        25.45         0.59 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       58.75        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J2 
        2.01        19.43        19.96        15.25        10.85        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       58.22       100.27        56.91        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JN 
       56.81        51.52        35.67        38.99        26.43        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-4A-A93Y TCGA-A4-7287 
       31.20        29.36        25.58         5.29        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
       61.05         0.10        35.18         0.23        29.46        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       23.31         0.76        14.33        12.46        16.96         8.48 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        8.28        12.46        58.45        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 
       49.25        19.56        21.67        16.87        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        6.58        10.09        34.49        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        15.12        43.99         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 
       30.28        26.04        13.25        10.88         7.66         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 
      123.62        48.26        93.34        44.84        61.28        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
      129.86        37.55        24.46        13.78         3.75         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
       40.77        79.86        61.02        54.90        34.19        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       10.68         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
       34.82        13.68        25.84         6.38        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK 
        0.89        11.21         4.60        13.41        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
        5.49        16.80        19.99        85.78        88.24        67.17 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z 
       21.34        16.34        12.36         0.13        11.41        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       30.38        27.65        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL 
       99.78        87.22        42.94        84.95        92.58        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM 
       50.60        78.90        12.85        47.44        33.04        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       19.00        38.63        26.47        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PX 
       14.83        21.93        86.27        38.86        30.67        27.39 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       26.01        18.64        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
        6.74        13.28 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            151.96             194.79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             25.68              32.61 
[1] "0.1 - 152.0 (25.7)" "0.1 - 194.8 (32.6)"
[1] "hr=" "1.2"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        98       30        55       35
  20P GAIN WILD-TYPE     350       73       135       65
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 98                350
  STAGE II                30                 73
  STAGE III               55                135
  STAGE IV                35                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED   102  35  77   8
  20P GAIN WILD-TYPE 360  88 174   7
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1              102                360
  T2               35                 88
  T3               77                174
  T4                8                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20P GAIN MUTATED    74  14   2
  20P GAIN WILD-TYPE 243  29   4
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               74                243
  N1               14                 29
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   126  30
  20P GAIN WILD-TYPE 416  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    126   30
  20P GAIN WILD-TYPE  416   59
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              126                416
  1               30                 59
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    56 168
  20P GAIN WILD-TYPE 231 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     56  168
  20P GAIN WILD-TYPE  231  404
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               56                231
  MALE                168                404
[1] 2 2
[1] FALSE
D36V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20P GAIN MUTATED                   21                               112
  20P GAIN WILD-TYPE                 45                               412
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20P GAIN MUTATED                                      91
  20P GAIN WILD-TYPE                                   178
D36V9, multiclass
                                       clus
vv                                      20P GAIN MUTATED 20P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  112                412
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               91                178
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V10, continuous
D36V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     3
  20P GAIN WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          22   191
  20P GAIN WILD-TYPE                        94   511
D36V12, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 12
  BLACK OR AFRICAN AMERICAN                      22                 94
  WHITE                                         191                511
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V13, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     8 157
  20P GAIN WILD-TYPE  34 440
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8  157
  20P GAIN WILD-TYPE   34  440
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 34
  NOT HISPANIC OR LATINO              157                440
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   164  57
  20Q GAIN WILD-TYPE 468 154
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               221                622 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                57                154 
$`20Q GAIN MUTATED`
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8339 TCGA-KL-8341 TCGA-KL-8346 
      141.73       137.06        98.96        28.11        24.79        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
      151.96        49.97        25.91       104.52         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
       11.21        42.35        10.68        74.93        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 
       86.10        77.85        12.66         0.53        24.16        49.08 
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3372 TCGA-A3-3374 
       37.15        24.69        52.93        42.97        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 
       18.87        65.52        84.36        66.31        72.07        57.37 
TCGA-AK-3445 TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
       42.08        45.93         1.41         1.38         3.62        65.10 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 
       19.73        43.96        46.59        52.21         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5094 
       36.53        10.09        40.70        10.29        29.03        10.95 
TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5832 TCGA-B4-5838 
       52.54        19.30        11.80        21.60         0.23         5.46 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 
       25.55        25.91        23.01        20.91        27.02         0.53 
TCGA-B8-A54I TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 
        4.93         0.43        89.36        64.27         0.07        93.99 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 
       74.17        62.86        31.89        11.31         5.98        13.15 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4803 TCGA-BP-4804 
       68.38        15.78        10.98        37.25         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4992 
       71.41         6.74        58.98        46.45        31.30        16.47 
TCGA-BP-4994 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5178 
       43.00        36.23        28.87         1.78        30.64        62.86 
TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 
       37.22        31.79        19.82        34.95        46.55        11.05 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 
       79.66        47.18        74.27        77.36        66.21        61.91 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 
       59.44        47.67        49.97        51.29        49.28        63.88 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 
       84.66        22.32        61.91        66.31        74.66         1.35 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4866 
       46.16        47.08        69.21         6.77        14.66        61.41 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 
       56.28        47.01        10.85        57.21         1.94        31.10 
TCGA-CZ-5984 TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9JG 
       67.96         3.91         7.04        75.55         4.57        54.64 
TCGA-2Z-A9JM TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-A4-7286 
       30.71        16.18        22.49         0.13        12.82        18.21 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       19.13         0.89        16.64        30.48        25.64        23.97 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-3466 
       19.63        19.73        16.31        15.75        12.99         9.63 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       76.64        13.55         2.20         7.33        24.56         3.55 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4117 TCGA-B9-4617 
       33.83        30.58        34.49        12.46         0.46         1.15 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 
       22.06         0.16        17.49        22.92        21.63        25.35 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7062 
        0.95        11.97         2.76        96.92        50.40         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6133 
       11.61        13.61        35.93        14.63        80.88        51.19 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6797 
       19.00        13.08         2.40         4.01        39.25        25.15 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40Y 
       17.98        17.33         3.68        68.12        11.84         2.04 
TCGA-IZ-8195 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 
       22.26        11.97        29.10        34.29        20.25         0.36 
TCGA-P4-A5EA TCGA-P4-AAVK TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        6.61        52.27        78.90        17.75        14.07        47.90 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PP 
       28.80        27.06        16.31        41.62        48.30         0.53 
TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A8S0 
       25.68        12.99        29.00        15.91         6.02 

$`20Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       102.81        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       86.56        66.54        73.91        71.41        28.80        54.74 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 
       23.28        44.91        28.80        47.24       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       31.33       129.37        23.47        87.91        25.48        65.19 
TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
        3.55        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 
      100.87        76.90        79.04        92.71        16.67       103.27 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       57.17        61.58        63.95        12.16        36.82        47.21 
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       39.16        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        18.44        88.37        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 
       10.49        28.70        74.63        74.76        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       20.71        18.64        28.31        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
       73.08        15.78        60.92        68.61        67.20        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        58.49        48.69        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        1.41         3.32         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       19.00         7.82         5.98         2.14         3.16         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        20.25        15.72         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 
       33.50        16.77        14.93        54.48        29.10        78.44 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       11.64        65.29        39.45        26.07         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       52.08        15.95        62.89        90.87        90.48        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       29.95        35.90        26.20        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        9.57         5.75         1.25         0.53         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       24.66        17.19        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60         6.38        14.27        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         8.42        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4169 
       90.28       101.06        93.34        32.61        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        61.78        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       15.16        18.48        52.24        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       56.91        11.64        60.95        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       36.39        36.95         6.94        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22        61.51        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       36.07        33.34        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       46.45         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 
       38.70        37.02        27.62        37.48        35.21        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        6.35        79.30        74.20        52.27         9.63        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       27.02        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        31.27         0.95        59.84        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
       21.24        83.97        49.25        75.06        64.27        71.87 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       50.24        56.35        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 
       38.56        45.14         3.06         4.57        18.81        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       79.89        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 
        5.39        85.78        73.18        78.18       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 
      103.43        18.77        25.45         0.59        58.75        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04         5.46        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       23.74        18.44        55.33        56.94        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       21.76        47.54        22.52         2.40        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        66.02        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       19.96        15.25        10.85        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
       56.91        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       35.67        38.99        26.43        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       25.58         5.29        11.57        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       35.18         0.23        29.46        23.28        23.31         0.76 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP 
       14.33        12.46        16.96         8.48         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
       58.45        30.35        25.08        44.61        49.25        19.56 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3926 
       21.67        16.87        16.77         0.46         6.58        10.09 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 
       10.16        50.50        28.18        26.40        20.61        15.12 
TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI 
       43.99         2.10        19.23         6.81        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 
       40.83        26.04        30.28        26.04        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 
        7.66         7.92       123.62        48.26        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       61.28        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
        7.04         7.17       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-DZ-6135 
        3.75         3.02        40.77        79.86        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       34.19        24.89        10.68         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       48.62        11.05        34.82        13.68        25.84         6.38 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH 
       12.43        17.95         0.89        11.21         4.60        13.41 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       88.24        67.17        21.34        16.34        12.36         0.13 
TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A855 TCGA-MH-A856 
       11.41        27.78        30.38        27.65        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z8 TCGA-SX-A71S TCGA-SX-A71U 
       92.58        16.01        50.60        12.85        47.44        33.04 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 
       11.93        19.00        38.63        26.47        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       30.67        27.39        26.01        18.64        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       15.62        25.28         6.74        13.28 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            151.96             194.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
             25.91              31.97 
[1] "0.1 - 152.0 (25.9)" "0.1 - 194.8 (32.0)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED        98       30        58       35
  20Q GAIN WILD-TYPE     350       73       132       65
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                 98                350
  STAGE II                30                 73
  STAGE III               58                132
  STAGE IV                35                 65
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED   103  35  80   7
  20Q GAIN WILD-TYPE 359  88 171   8
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1              103                359
  T2               35                 88
  T3               80                171
  T4                7                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  20Q GAIN MUTATED    75  16   2
  20Q GAIN WILD-TYPE 242  27   4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               75                242
  N1               16                 27
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   130  30
  20Q GAIN WILD-TYPE 412  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    130   30
  20Q GAIN WILD-TYPE  412   59
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              130                412
  1               30                 59
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    59 169
  20Q GAIN WILD-TYPE 228 403
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     59  169
  20Q GAIN WILD-TYPE  228  403
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               59                228
  MALE                169                403
[1] 2 2
[1] FALSE
D37V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20Q GAIN MUTATED                   21                               114
  20Q GAIN WILD-TYPE                 45                               410
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20Q GAIN MUTATED                                      93
  20Q GAIN WILD-TYPE                                   176
D37V9, multiclass
                                       clus
vv                                      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  114                410
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               93                176
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V10, continuous
D37V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     4
  20Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          21   195
  20Q GAIN WILD-TYPE                        95   507
D37V12, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                 11
  BLACK OR AFRICAN AMERICAN                      21                 95
  WHITE                                         195                507
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V13, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8 160
  20Q GAIN WILD-TYPE  34 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  160
  20Q GAIN WILD-TYPE   34  437
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 34
  NOT HISPANIC OR LATINO              160                437
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    51  20
  21Q GAIN WILD-TYPE 581 191
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                71                772 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                20                191 
$`21Q GAIN MUTATED`
TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8433 TCGA-KN-8436 TCGA-A3-3316 TCGA-A3-3322 
      151.96        31.33        11.21        42.35        49.08        48.59 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3445 TCGA-B0-4690 TCGA-B0-4696 
       24.16        18.87        66.31        42.08         1.41        28.47 
TCGA-B0-4844 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5116 
       10.29        15.95        90.87        52.54        11.80        21.60 
TCGA-B0-5696 TCGA-B4-5832 TCGA-B8-5163 TCGA-B8-A54F TCGA-BP-4167 TCGA-BP-4176 
       56.78         0.23        27.02        17.06        89.36        64.27 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4763 TCGA-BP-4781 
        0.07        93.99        31.89        11.31        41.75        68.38 
TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4995 TCGA-BP-5173 TCGA-BP-5178 TCGA-BP-5185 
       58.98        31.30        45.07         1.78        62.86        37.22 
TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4873 TCGA-CJ-5676 TCGA-CJ-5679 
       31.79        46.55        14.17        74.27        84.66        22.32 
TCGA-CJ-6027 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5461 
       60.99        74.66        46.16        61.41        47.01        10.85 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-EU-5905 
        1.94        31.10        12.16        37.15        66.02         3.91 
TCGA-2K-A9WE TCGA-2Z-A9JS TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A6HP TCGA-AT-A5NU 
        7.04        16.18        23.97        23.31        12.46         2.20 
TCGA-B1-A47O TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5892 TCGA-F9-A8NY TCGA-G7-A8LC 
       16.87         0.46         0.16        11.97         1.18        17.33 
TCGA-HE-A5NJ TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PK TCGA-UZ-A9Q0 
       56.75         6.61        14.07        60.03        12.99 

$`21Q GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       51.06       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
       19.33         2.50        59.08       115.00       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 
       39.16        24.16        49.02        37.15        49.58        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        24.69        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       84.36        73.08        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 
       67.20        57.37        46.78        48.36        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        4.57         2.53         3.48        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        11.64        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       62.89        90.48        30.48        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       15.78        46.68        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67         9.57         5.75         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G 
        0.53        34.39        14.30        27.29        29.88         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85         0.43        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        12.33        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62         5.98        44.15        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       43.00        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       59.84        63.25        73.22        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       63.88        72.00        79.89        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       78.18         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       25.45         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       56.94        55.33        10.22        21.76        57.21        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       22.52         2.40        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       65.88        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9J1 
        2.01        19.43        19.96        15.25        10.85        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       25.58         5.29        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       18.21        19.63        61.05         0.10        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8312 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.28         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       44.61        49.25        19.56         7.33        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         1.15        15.12        43.99        22.06 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
        2.10        19.23         6.81        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       25.35        13.25        10.88         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         0.43         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK 
       11.21         4.60        68.12        13.41        11.84        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-WN-A9G9 
       38.86        52.11        30.67        25.68        27.39        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.07               0.10 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            151.96             194.79 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             28.47              30.53 
[1] "0.1 - 152.0 (28.5)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1.3"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        34        6        21       10
  21Q GAIN WILD-TYPE     414       97       169       90
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 34                414
  STAGE II                 6                 97
  STAGE III               21                169
  STAGE IV                10                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED    36   7  28   2
  21Q GAIN WILD-TYPE 426 116 223  13
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               36                426
  T2                7                116
  T3               28                223
  T4                2                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  21Q GAIN MUTATED    23   3   0
  21Q GAIN WILD-TYPE 294  40   6
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               23                294
  N1                3                 40
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    42  10
  21Q GAIN WILD-TYPE 500  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     42   10
  21Q GAIN WILD-TYPE  500   79
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               42                500
  1               10                 79
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    22  51
  21Q GAIN WILD-TYPE 265 521
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     22   51
  21Q GAIN WILD-TYPE  265  521
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               22                265
  MALE                 51                521
[1] 2 2
[1] FALSE
D38V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  21Q GAIN MUTATED                    4                                50
  21Q GAIN WILD-TYPE                 62                               474
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  21Q GAIN MUTATED                                      19
  21Q GAIN WILD-TYPE                                   250
D38V9, multiclass
                                       clus
vv                                      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                   50                474
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               19                250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V10, continuous
D38V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                1    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           5    65
  21Q GAIN WILD-TYPE                       111   637
D38V12, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       5                111
  WHITE                                          65                637
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V13, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  52
  21Q GAIN WILD-TYPE  38 545
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   52
  21Q GAIN WILD-TYPE   38  545
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               52                545
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    46  15
  22Q GAIN WILD-TYPE 586 196
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                61                782 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                15                196 
$`22Q GAIN MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 
       38.07       141.73       137.06        24.79        62.37        49.97 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 
       23.47        25.91         3.55         0.99        52.27        11.21 
TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       42.35        74.93        16.67        80.38        87.78        86.10 
TCGA-KO-8414 TCGA-A3-3306 TCGA-A3-3319 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 
       77.85        36.82        37.15        43.20        18.87        72.07 
TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-5081 TCGA-B0-5099 TCGA-B0-5102 
       57.37         3.32         3.62        11.90        15.95        90.87 
TCGA-B0-5113 TCGA-B0-5400 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4166 TCGA-BP-4174 
       11.80        37.22         0.23         5.46         0.43        61.78 
TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4765 
       64.27         0.07        74.17        31.89        11.31        71.80 
TCGA-BP-4781 TCGA-BP-4975 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5178 TCGA-BP-5185 
       68.38        47.11        43.00         1.78        62.86        37.22 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 
       19.82        34.95        51.29        49.28        63.88        84.66 
TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4860 TCGA-CZ-5984 TCGA-BQ-5892 
       61.91        66.31        74.66         6.77        67.96        11.97 
TCGA-G7-A8LB 
       17.98 

$`22Q GAIN WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        28.11        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
       65.19       104.52        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8411 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      103.27        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       53.29        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        7.30        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
        2.24        21.86        52.08        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        19.30        35.90        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 
       17.59         1.94        16.21        18.21        21.44        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67         9.57         5.75         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        4.64         0.36         0.23        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
       23.01        20.91        23.74         1.18        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       32.61        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        21.21        15.16        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 
       77.62         5.98        44.15        41.75        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4976 
       14.24        48.89        49.38        45.50         7.23        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       74.40        49.15        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        44.55        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        47.67        49.97        58.92        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00        79.89        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       18.15        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        69.21        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       57.21        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        80.19        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.88         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            141.73             194.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             42.35              29.90 
[1] "0.1 - 141.7 (42.4)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED        23       12        16       11
  22Q GAIN WILD-TYPE     425       91       174       89
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                 23                425
  STAGE II                12                 91
  STAGE III               16                174
  STAGE IV                11                 89
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED    23  13  22   4
  22Q GAIN WILD-TYPE 439 110 229  11
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               23                439
  T2               13                110
  T3               22                229
  T4                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"
                    vv
clus                  N0  N1  N2
  22Q GAIN MUTATED    30   3   1
  22Q GAIN WILD-TYPE 287  40   5
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               30                287
  N1                3                 40
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    44   8
  22Q GAIN WILD-TYPE 498  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     44    8
  22Q GAIN WILD-TYPE  498   81
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               44                498
  1                8                 81
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    17  45
  22Q GAIN WILD-TYPE 270 527
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     17   45
  22Q GAIN WILD-TYPE  270  527
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               17                270
  MALE                 45                527
[1] 2 2
[1] FALSE
D39V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  22Q GAIN MUTATED                   19                                40
  22Q GAIN WILD-TYPE                 47                               484
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  22Q GAIN MUTATED                                       3
  22Q GAIN WILD-TYPE                                   266
D39V9, multiclass
                                       clus
vv                                      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  19                 47
  KIDNEY CLEAR CELL RENAL CARCINOMA                   40                484
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                3                266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V10, continuous
D39V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     1
  22Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           2    59
  22Q GAIN WILD-TYPE                       114   643
D39V12, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          59                643
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V13, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     4  33
  22Q GAIN WILD-TYPE  38 564
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4   33
  22Q GAIN WILD-TYPE   38  564
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               33                564
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED    94  18
  XP GAIN WILD-TYPE 538 193
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              112               731 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               18               193 
$`XP GAIN MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 
       62.37        23.47        25.91         3.55        11.21        87.78 
TCGA-KO-8413 TCGA-A3-3382 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 
       86.10        18.87        73.08        66.31        67.20        42.08 
TCGA-AK-3453 TCGA-B0-4827 TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 
       45.93        29.10        19.30         4.93       101.06        61.78 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 TCGA-BP-4799 
        0.07        93.99        11.31        12.30        10.82        37.25 
TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 
       58.98         3.88        11.05        69.86        50.24        18.15 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-EU-5905 
       74.66        46.16        56.28        57.21         1.94         3.91 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ 
       75.55        59.01        58.22       100.27        56.91        25.58 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.97        23.31         0.76        19.63        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU 
       16.31        15.75        12.46        76.64        13.55         2.20 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 
       21.67        24.56         6.58        30.58        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W9 TCGA-B9-A8YH 
       28.18         0.46         1.15        43.99         0.16        17.49 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 
       47.80        25.35         0.95         7.92        48.26        96.92 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF 
        7.04         3.81        35.93        40.77        51.19         2.40 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 
        1.18        51.78        39.25         6.38        17.98       194.79 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD 
       17.95        68.12        11.84        56.75         5.49        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB 
       29.10        11.41        34.29        27.78        87.22        84.95 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       52.27        16.01        17.75        33.04        28.80        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU 
       16.31        41.62        26.47        48.30        60.03        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       25.68        27.39        12.99        15.91 

$`XP GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       84.36        15.78        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       46.78        48.36        40.01        58.49        48.69        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 
       40.44        36.53        14.93        54.48        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67         9.57         5.75         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        1.74         8.42        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 
      111.02        85.51        94.72        90.28        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       62.07        80.68        37.25        21.21        15.16        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       12.23        31.89        12.33        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       48.95        36.53        20.38        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       25.81        36.95        27.22        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        53.52        58.95        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        59.44        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       25.25        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       18.77        25.45         0.59        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       21.76        47.54        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       31.20        29.36         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E 
       29.46        25.64        23.28        19.73        12.46         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.99         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 
       44.61        49.25        19.56         7.33        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77         0.46        33.83        10.09        34.49        12.46 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
       26.40        20.61        15.12        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        6.81        14.86        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       30.28        26.04        13.25        10.88         7.66        11.97 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
       49.84        26.27        20.12        11.28         7.63         7.17 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.61        13.61       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
        3.75        14.63         3.02        79.86        80.88        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
        0.43         4.01        48.62        11.05        34.82        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 
       13.68        25.84        17.33        16.90        80.65        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        4.60        13.41        73.25        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       12.36         0.13        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 
       12.13        25.97        21.44        15.48        99.78        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
        6.61        92.58        50.60        78.90        12.85        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU 
       47.90        47.44        27.06        11.93        38.63        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       18.02        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       52.11        26.01        29.00        18.64        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           194.79            151.96 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           25.795            31.270 
[1] "0.1 - 194.8 (25.8)" "0.1 - 152.0 (31.3)"
[1] "hr=" "1.5"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED        73       11        12       14
  XP GAIN WILD-TYPE     375       92       178       86
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                73               375
  STAGE II               11                92
  STAGE III              12               178
  STAGE IV               14                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP GAIN MUTATED    75  16  21   3
  XP GAIN WILD-TYPE 387 107 230  12
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              75               387
  T2              16               107
  T3              21               230
  T4               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"
                   vv
clus                 N0  N1  N2
  XP GAIN MUTATED    33   4   0
  XP GAIN WILD-TYPE 284  39   6
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              33               284
  N1               4                39
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V6, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    48  11
  XP GAIN WILD-TYPE 494  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     48   11
  XP GAIN WILD-TYPE  494   78
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              48               494
  1              11                78
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    28  89
  XP GAIN WILD-TYPE 259 483
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     28   89
  XP GAIN WILD-TYPE  259  483
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              28               259
  MALE                89               483
[1] 2 2
[1] FALSE
D40V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XP GAIN MUTATED                    7                                29
  XP GAIN WILD-TYPE                 59                               495
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XP GAIN MUTATED                                      81
  XP GAIN WILD-TYPE                                   188
D40V9, multiclass
                                       clus
vv                                      XP GAIN MUTATED XP GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  7                59
  KIDNEY CLEAR CELL RENAL CARCINOMA                  29               495
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              81               188
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V10, continuous
D40V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  2     3
  XP GAIN WILD-TYPE                                0    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          15    91
  XP GAIN WILD-TYPE                       101   611
D40V12, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                     15               101
  WHITE                                         91               611
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V13, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5  88
  XP GAIN WILD-TYPE  37 509
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5   88
  XP GAIN WILD-TYPE   37  509
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                37
  NOT HISPANIC OR LATINO              88               509
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    94  19
  XQ GAIN WILD-TYPE 538 192
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              113               730 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19               192 
$`XQ GAIN MUTATED`
TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 
       62.37        23.47        25.91         3.55        11.21        87.78 
TCGA-KO-8413 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B0-4827 
       86.10        73.08        66.31        67.20        45.93        29.10 
TCGA-B0-5080 TCGA-B0-5109 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4337 
       11.24        19.30         4.93       101.06        61.78         0.07 
TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4799 TCGA-BP-4969 TCGA-BP-4989 TCGA-BP-5176 
       93.99        11.31        37.25        58.98         3.88        52.27 
TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 
       11.05        69.86        50.24        18.15        74.66        46.16 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-EU-5905 TCGA-MM-A84U 
       56.28        56.94        57.21         1.94         3.91        15.25 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JQ 
       75.55        59.01        58.22       100.27        56.91        25.58 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.97        23.31         0.76        19.63        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU 
       16.31        15.75        12.46        76.64        13.55         2.20 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 
       21.67        24.56         6.58        30.58        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A5W9 
       28.18        20.61         0.46         1.15        43.99         0.16 
TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 
       17.49        47.80        25.35         0.95         7.92        48.26 
TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7963 TCGA-DZ-6133 
       96.92         7.04         3.81        35.93        40.77        51.19 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB 
        2.40         1.18        51.78        39.25         6.38        17.98 
TCGA-GL-6846 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
      194.79        17.95        68.12        11.84        56.75         5.49 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-P4-A5E7 
       11.97        29.10        11.41        34.29        27.78        87.22 
TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A71V 
       84.95        52.27        16.01        17.75        33.04        28.80 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK 
       19.00        16.31        41.62        26.47        48.30        60.03 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A895 
       30.67        25.68        27.39        12.99        15.91 

$`XQ GAIN WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       51.06        31.33       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       29.10        84.36        15.78        60.92        72.07        68.61 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       28.04        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       29.95        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       17.06         1.74         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
       14.17       111.02        85.51        94.72        90.28        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       36.39        10.98        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.51         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.78        74.20        30.64         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
       75.88        65.69        54.61        53.52        58.95        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        59.44        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        25.25        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        66.31        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        25.45         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       23.74        18.44        55.33        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 
       10.22        21.76        47.54        22.52         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
       35.87         2.01        19.43        19.96        10.85         7.04 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       31.20        29.36         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E 
       29.46        25.64        23.28        19.73        12.46         8.48 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.99         9.63        58.45        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A654 
       44.61        49.25        19.56         7.33        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
       16.77         0.46        33.83        10.09        34.49        12.46 
TCGA-B9-4115 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       26.40        15.12        22.06         2.10        19.23         6.81 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 
       26.04        13.25        10.88         7.66        11.97         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 
       26.27        20.12        11.28         7.63         7.17        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
       14.63         3.02        79.86        80.88        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G 
       34.19        19.00        24.89        10.68        13.08         0.43 
TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        4.01        48.62        11.05        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 
       25.84        17.33        16.90        80.65        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43         0.89        11.21         4.60 
TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       13.41        73.25        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
        0.13        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R 
       92.58        50.60        78.90        12.85        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SU TCGA-UN-AAZ9 
       47.44        27.06        11.93        38.63        43.76        18.02 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       26.01        29.00        18.64        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           194.79            151.96 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           25.910            31.235 
[1] "0.1 - 194.8 (25.9)" "0.1 - 152.0 (31.2)"
[1] "hr=" "1.4"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        73       11        12       14
  XQ GAIN WILD-TYPE     375       92       178       86
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                73               375
  STAGE II               11                92
  STAGE III              12               178
  STAGE IV               14                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ GAIN MUTATED    75  17  22   2
  XQ GAIN WILD-TYPE 387 106 229  13
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              75               387
  T2              17               106
  T3              22               229
  T4               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XQ GAIN MUTATED    32   4   0
  XQ GAIN WILD-TYPE 285  39   6
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              32               285
  N1               4                39
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V6, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    46  12
  XQ GAIN WILD-TYPE 496  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     46   12
  XQ GAIN WILD-TYPE  496   77
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              46               496
  1              12                77
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    29  89
  XQ GAIN WILD-TYPE 258 483
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     29   89
  XQ GAIN WILD-TYPE  258  483
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              29               258
  MALE                89               483
[1] 2 2
[1] FALSE
D41V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XQ GAIN MUTATED                    7                                29
  XQ GAIN WILD-TYPE                 59                               495
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XQ GAIN MUTATED                                      82
  XQ GAIN WILD-TYPE                                   187
D41V9, multiclass
                                       clus
vv                                      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  7                59
  KIDNEY CLEAR CELL RENAL CARCINOMA                  29               495
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              82               187
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V10, continuous
D41V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  2     2
  XQ GAIN WILD-TYPE                                0    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          17    91
  XQ GAIN WILD-TYPE                        99   611
D41V12, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                     17                99
  WHITE                                         91               611
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V13, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5  90
  XQ GAIN WILD-TYPE  37 507
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5   90
  XQ GAIN WILD-TYPE   37  507
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                37
  NOT HISPANIC OR LATINO              90               507
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   104  34
  1P LOSS WILD-TYPE 528 177
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              138               705 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               34               177 
$`1P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 
      151.96        44.91        47.24        49.97       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 
       87.91        25.48        65.19       104.52         0.99        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 
       19.33         2.50        59.08       115.00        42.35        76.90 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        80.38       103.27 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3316 
       77.85        57.17        61.58        63.95        24.16        49.08 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 
       53.29        43.20        18.64        84.36        72.07        57.37 
TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4821 
       40.01        12.13        40.70         1.38         3.62        40.44 
TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5098 
       36.53        68.71        65.29        36.85         7.30        52.08 
TCGA-B0-5102 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-4098 
       90.87        17.59        14.76        39.55        32.61         1.68 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 
        0.53         5.46        17.19         6.38        64.27        21.21 
TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4968 
       74.17        12.33        13.15        60.59        68.38        57.40 
TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5201 TCGA-CJ-4635 
       25.81        43.00        37.02         1.78        31.27        46.55 
TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 
       65.69        64.27        27.65        59.44        47.67        49.28 
TCGA-CJ-5678 TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5462 
       18.87        66.31         6.77        61.41        55.33        10.22 
TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X 
       31.10         4.18        35.87        54.64        51.52        12.82 
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 
       18.21         0.10        29.46        12.99         7.33        10.09 
TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7055 
        6.81        86.76        21.63         2.76       123.62        26.27 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 
       10.68        13.08        25.15        25.84        17.33        27.65 
TCGA-HE-A5NK TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       73.25         6.61        12.85        14.07        18.02        86.27 

$`1P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
       23.28        28.80        51.06        31.33        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 
        3.55        52.27        11.21       100.87        10.68        87.78 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       86.10        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       39.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 
       38.99        24.69        37.38        48.82        21.86        34.29 
TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       31.07         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.63        74.76        24.16        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 
        0.10        11.18        10.62       109.91        29.10        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
       66.31        15.78        60.92        68.61        67.20        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       22.45        37.58        38.40        31.27        28.04         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
       19.00        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77         6.02        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        11.64        10.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
        2.27        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       21.86        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
        1.94        16.21        18.21        21.44        37.22        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 
       60.33        84.92        90.12        56.94        52.77       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       97.41        35.90        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.23         1.25         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        27.55        25.05        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
        0.85        24.23        17.16        16.60        14.27         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        80.68        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       61.97        13.51        56.91        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       31.30        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
        6.35        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95        59.84        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       77.36        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       50.01        24.66        39.45        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        58.92        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       79.89        84.66        25.71        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
       74.66         1.35       105.93        83.90       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 
       14.66        60.59        63.39        93.04         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        56.28        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       55.33        47.01        10.85        21.76        57.21        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40         1.94        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        70.13         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 
        0.13        11.57        19.63        61.05        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        0.89         0.23        16.64        30.48        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       25.08        44.61        49.25         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06         2.10        19.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        7.92        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        19.00        24.89         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92         3.68         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.10              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           151.96            194.79 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            44.02             28.80 
[1] "0.1 - 152.0 (44.0)" "0.1 - 194.8 (28.8)"
[1] "hr=" "1.4"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        55       34        33       14
  1P LOSS WILD-TYPE     393       69       157       86
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                55               393
  STAGE II               34                69
  STAGE III              33               157
  STAGE IV               14                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    59  36  38   5
  1P LOSS WILD-TYPE 403  87 213  10
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              59               403
  T2              36                87
  T3              38               213
  T4               5                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  1P LOSS MUTATED    64   9   2
  1P LOSS WILD-TYPE 253  34   4
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              64               253
  N1               9                34
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    93   9
  1P LOSS WILD-TYPE 449  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     93    9
  1P LOSS WILD-TYPE  449   80
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              93               449
  1               9                80
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    48  91
  1P LOSS WILD-TYPE 239 481
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     48   91
  1P LOSS WILD-TYPE  239  481
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              48               239
  MALE                91               481
[1] 2 2
[1] FALSE
D42V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1P LOSS MUTATED                   53                                59
  1P LOSS WILD-TYPE                 13                               465
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1P LOSS MUTATED                                      27
  1P LOSS WILD-TYPE                                   242
D42V9, multiclass
                                       clus
vv                                      1P LOSS MUTATED 1P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 53                13
  KIDNEY CLEAR CELL RENAL CARCINOMA                  59               465
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              27               242
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V10, continuous
D42V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     4
  1P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          18   111
  1P LOSS WILD-TYPE                        98   591
D42V12, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                11
  BLACK OR AFRICAN AMERICAN                     18                98
  WHITE                                        111               591
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V13, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10  80
  1P LOSS WILD-TYPE  32 517
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10   80
  1P LOSS WILD-TYPE   32  517
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                32
  NOT HISPANIC OR LATINO              80               517
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    83  23
  1Q LOSS WILD-TYPE 549 188
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              106               737 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               23               188 
$`1Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 
       44.91        47.24        49.97       123.12       129.37        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.48        65.19       104.52         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
       19.33        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 
       57.17        61.58        63.95        43.20        18.64        84.36 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4698 
       72.07        57.37        12.13        40.70        28.47         1.38 
TCGA-B0-4699 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 
        3.62        40.44        36.53        68.71        65.29        36.85 
TCGA-B0-5084 TCGA-B0-5102 TCGA-B0-5117 TCGA-B2-3923 TCGA-B4-5838 TCGA-B8-4619 
        7.30        90.87        17.59        32.61         5.46        17.19 
TCGA-B8-5549 TCGA-BP-4334 TCGA-BP-4353 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4968 
        6.38        21.21        12.33        13.15        60.59        57.40 
TCGA-BP-4986 TCGA-BP-4994 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CW-5588 
       25.81        43.00        59.44        47.67        49.28        66.31 
TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-2Z-A9JG TCGA-4A-A93X 
        6.77        61.41        55.33        31.10        54.64        12.82 
TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-A5W8 
       18.21         0.10         7.33        16.77        10.09         6.81 
TCGA-BQ-5894 TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 
        2.76        13.08        25.15        25.84        17.33        27.65 
TCGA-HE-A5NK TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-UN-AAZ9 
       73.25         6.61        12.85        18.02 

$`1Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 
      109.22        23.28        28.80        51.06        31.33        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55         2.50        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       87.78        86.10        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       53.29        55.76        20.71        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62       109.91        29.10        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       60.92        68.61        67.20        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        31.27        28.04         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 
        1.41         4.57         2.53         3.48        19.00        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       14.93        54.48        29.10        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.29        39.45        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       61.32        97.41        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       31.30        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       73.18        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        5.46        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       56.28        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 
        0.13        11.57        19.63        61.05        35.18        19.13 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        0.89         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
        8.28        12.99        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 
       19.56        21.67        24.56        16.87         3.55         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 
       15.12        43.99        22.06         2.10        19.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95        11.97         7.92       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       13.68         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92         3.68         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       52.27        16.01        50.60        78.90        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.10              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           151.96            194.79 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           47.455            29.030 
[1] "0.1 - 152.0 (47.5)" "0.1 - 194.8 (29.0)"
[1] "hr=" "1.7"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        42       30        22       10
  1Q LOSS WILD-TYPE     406       73       168       90
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                42               406
  STAGE II               30                73
  STAGE III              22               168
  STAGE IV               10                90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1Q LOSS MUTATED    44  30  28   4
  1Q LOSS WILD-TYPE 418  93 223  11
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              44               418
  T2              30                93
  T3              28               223
  T4               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"
                   vv
clus                 N0  N1  N2
  1Q LOSS MUTATED    55   7   2
  1Q LOSS WILD-TYPE 262  36   4
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              55               262
  N1               7                36
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    71   6
  1Q LOSS WILD-TYPE 471  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     71    6
  1Q LOSS WILD-TYPE  471   83
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              71               471
  1               6                83
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    40  67
  1Q LOSS WILD-TYPE 247 505
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     40   67
  1Q LOSS WILD-TYPE  247  505
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              40               247
  MALE                67               505
[1] 2 2
[1] FALSE
D43V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1Q LOSS MUTATED                   52                                37
  1Q LOSS WILD-TYPE                 14                               487
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1Q LOSS MUTATED                                      18
  1Q LOSS WILD-TYPE                                   251
D43V9, multiclass
                                       clus
vv                                      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 52                14
  KIDNEY CLEAR CELL RENAL CARCINOMA                  37               487
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              18               251
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V10, continuous
D43V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     4
  1Q LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                           9    89
  1Q LOSS WILD-TYPE                       107   613
D43V12, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                11
  BLACK OR AFRICAN AMERICAN                      9               107
  WHITE                                         89               613
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V13, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     7  65
  1Q LOSS WILD-TYPE  35 532
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7   65
  1Q LOSS WILD-TYPE   35  532
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO              65               532
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    50  11
  2P LOSS WILD-TYPE 582 200
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               61               782 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               200 
$`2P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       54.74       151.96        44.91        47.24        49.97       123.12 
TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      129.37        65.19       104.52        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
        2.50        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3374 TCGA-AK-3433 
       57.17        61.58        63.95        24.16        43.20        72.07 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4821 
       57.37        40.01        12.13        40.70         3.62        40.44 
TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4334 TCGA-BP-4994 TCGA-BP-5175 TCGA-4A-A93X 
       17.59        32.61        21.21        43.00        30.64        12.82 
TCGA-BQ-5875 
       86.76 

$`2P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 
      109.22        98.33        71.41        28.80        62.37        23.28 
TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       28.80        51.06        31.33        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55         0.99        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       87.78        86.10        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        31.27        28.04         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       96.36        89.49        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30         1.78        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           151.96            194.79 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            59.08             28.80 
[1] "2.5 - 152.0 (59.1)" "0.1 - 194.8 (28.8)"
[1] "hr=" "2.5"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED        20       24        14        4
  2P LOSS WILD-TYPE     428       79       176       96
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                20               428
  STAGE II               24                79
  STAGE III              14               176
  STAGE IV                4                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2P LOSS MUTATED    20  24  17   1
  2P LOSS WILD-TYPE 442  99 234  14
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              20               442
  T2              24                99
  T3              17               234
  T4               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"
                   vv
clus                 N0  N1  N2
  2P LOSS MUTATED    35   2   2
  2P LOSS WILD-TYPE 282  41   4
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              35               282
  N1               2                41
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V6, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    42   2
  2P LOSS WILD-TYPE 500  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     42    2
  2P LOSS WILD-TYPE  500   87
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              42               500
  1               2                87
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    27  36
  2P LOSS WILD-TYPE 260 536
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     27   36
  2P LOSS WILD-TYPE  260  536
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              27               260
  MALE                36               536
[1] 2 2
[1] FALSE
D44V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2P LOSS MUTATED                   46                                14
  2P LOSS WILD-TYPE                 20                               510
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2P LOSS MUTATED                                       3
  2P LOSS WILD-TYPE                                   266
D44V9, multiclass
                                       clus
vv                                      2P LOSS MUTATED 2P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 46                20
  KIDNEY CLEAR CELL RENAL CARCINOMA                  14               510
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               3               266
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V10, continuous
D44V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     3
  2P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           6    51
  2P LOSS WILD-TYPE                       110   651
D44V12, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                      6               110
  WHITE                                         51               651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V13, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  31
  2P LOSS WILD-TYPE  39 566
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   31
  2P LOSS WILD-TYPE   39  566
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              31               566
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    49  11
  2Q LOSS WILD-TYPE 583 200
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               60               783 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               200 
$`2Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       54.74       151.96        44.91        47.24        49.97       123.12 
TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      129.37        65.19       104.52        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 
        2.50        59.08       115.00        42.35        76.90        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 
       79.04        92.71        16.67        80.38       103.27        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 
       57.17        61.58        63.95        43.20        72.07        57.37 
TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4821 
       40.01        12.13        40.70        28.47         3.62        40.44 
TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4334 TCGA-BP-4994 TCGA-BP-5175 TCGA-4A-A93X 
       17.59        32.61        21.21        43.00        30.64        12.82 

$`2Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 
      109.22        98.33        71.41        28.80        62.37        23.28 
TCGA-KM-8441 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       28.80        51.06        31.33        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       25.91         3.55         0.99        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       87.78        86.10        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
       66.31        15.78        60.92        68.61        67.20        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       22.45        37.58        38.40        31.27        28.04         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        3.32         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       10.09        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       96.36        89.49        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30         1.78        74.20        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
        0.13        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.50              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           151.96            194.79 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           58.225            28.800 
[1] "2.5 - 152.0 (58.2)" "0.1 - 194.8 (28.8)"
[1] "hr=" "2.4"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED        19       24        14        4
  2Q LOSS WILD-TYPE     429       79       176       96
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                19               429
  STAGE II               24                79
  STAGE III              14               176
  STAGE IV                4                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED    19  24  17   1
  2Q LOSS WILD-TYPE 443  99 234  14
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              19               443
  T2              24                99
  T3              17               234
  T4               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"
                   vv
clus                 N0  N1  N2
  2Q LOSS MUTATED    35   2   2
  2Q LOSS WILD-TYPE 282  41   4
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              35               282
  N1               2                41
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V6, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    41   2
  2Q LOSS WILD-TYPE 501  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     41    2
  2Q LOSS WILD-TYPE  501   87
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              41               501
  1               2                87
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    26  36
  2Q LOSS WILD-TYPE 261 536
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     26   36
  2Q LOSS WILD-TYPE  261  536
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              26               261
  MALE                36               536
[1] 2 2
[1] FALSE
D45V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2Q LOSS MUTATED                   46                                14
  2Q LOSS WILD-TYPE                 20                               510
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2Q LOSS MUTATED                                       2
  2Q LOSS WILD-TYPE                                   267
D45V9, multiclass
                                       clus
vv                                      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 46                20
  KIDNEY CLEAR CELL RENAL CARCINOMA                  14               510
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               267
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V10, continuous
D45V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     3
  2Q LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           5    51
  2Q LOSS WILD-TYPE                       111   651
D45V12, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                      5               111
  WHITE                                         51               651
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V13, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  32
  2Q LOSS WILD-TYPE  39 565
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   32
  2Q LOSS WILD-TYPE   39  565
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              32               565
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   281 127
  3P LOSS WILD-TYPE 351  84
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              408               435 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              127                84 
$`3P LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8333 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 
      141.73        98.33        87.91       104.52         2.50        42.35 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-A3-3306 TCGA-A3-3307 
       80.38        77.85        57.17        12.66        36.82        47.21 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       39.16        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        24.69        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       34.29         4.50        52.93        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       42.97        82.32        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       53.29        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       10.62       109.91        29.10        66.31        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       72.07        68.61        67.20        42.08        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       28.73        22.45        38.40        31.27        28.04         1.41 
TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4703 TCGA-B0-4706 
        1.41         2.53         3.48        28.47         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       19.73         3.16         6.64        15.72        46.59         0.59 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        45.30        27.42         6.71        56.68        11.64 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       70.52        20.94        43.30        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 
        8.05         2.24        21.86        52.08        15.95        90.87 
TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       90.48        29.95        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
        1.94        16.21        21.44        14.76        79.17        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        52.77        39.55        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 
       47.97        96.36        89.49        61.32        35.90        12.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 
       11.77        32.98        21.57        16.67         9.57         0.23 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       16.80        27.16        25.55        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
        1.18        27.02         0.85         6.38         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       14.30        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4163 TCGA-BP-4164 
       16.27       111.02        85.51        94.72        93.34        32.61 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        61.78        64.27 
TCGA-BP-4325 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       97.45         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4758 TCGA-BP-4761 
       49.08        44.94        31.89        12.33        72.59         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        13.15         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4797 
       13.51        56.91        68.38        11.64        48.95        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4971 
       63.62        58.68        60.30        61.22        61.51        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         7.23        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
       33.34        46.45        31.30        25.81        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       18.51        37.02        27.62        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5178 
       48.10         6.35         1.78        74.20        52.27        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        27.02        33.24        13.41        24.62        33.47 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       63.25        73.22        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        79.66        74.27 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 
       75.06        64.27        71.87        66.21        61.91        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       30.64        51.52        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-4918 
       58.92        49.18        49.28        50.33        45.14         3.06 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5689 TCGA-CJ-6027 
       22.32        61.91        62.10        73.35        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 
       53.42        75.58        83.77         7.36        64.57        81.83 
TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        5.39        73.18        66.31        78.18        74.66       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       83.90        18.77        25.45         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
       58.75         6.77        14.66        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 
       57.21        47.54        22.52         1.94        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 
       45.96        12.16        37.15        66.28        56.84        66.02 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        6.77         4.18        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       19.96        15.25        10.85        54.64        51.52        38.99 
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 
        8.48        12.99        25.08         2.10        14.86         8.88 
TCGA-BQ-5882 TCGA-BQ-5892 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 
       21.63        11.97        79.86         4.01        17.33         3.68 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
        2.04         0.13        14.07        86.27        26.01         6.74 

$`3P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
       31.33       129.37        23.47        25.48        25.91        65.19 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 
        3.55         0.99        52.27        87.12        19.33        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       79.04        92.71        16.67        87.78       103.27        86.10 
TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3343 
       61.58        63.95        12.16         0.53        37.38        31.07 
TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 
       45.53        51.25        10.49        43.20        65.52        84.36 
TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 
       73.08        57.37        46.78        48.36        40.01        45.93 
TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4697 
       37.58        12.13        40.70         3.32         4.57        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4712 TCGA-B0-4714 
        1.38         3.62        65.10         7.82        43.96         3.25 
TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-4844 TCGA-B0-5080 
       20.25         5.52        68.71        53.88        10.29        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5100 TCGA-B0-5106 TCGA-B0-5107 
       11.90         7.30        25.32        62.89        52.54        30.48 
TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5705 
       19.30        17.59        18.21        37.22       112.80       120.59 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
       97.41        32.61         1.68        21.30        31.30        10.36 
TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
        5.75         0.53        27.55        25.05        24.66        17.19 
TCGA-B8-4621 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-A54D 
       25.91        24.23        17.16        16.60        14.27        27.29 
TCGA-B8-A54E TCGA-B8-A54K TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 
       29.88        15.42        14.17        90.28       101.06        99.85 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.24        54.90        53.42        21.21        15.16         0.07 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 
       12.23        11.31        33.99        31.33        12.30        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4784 
       77.62        44.15        61.68        10.82        60.59        60.95 
TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4967 
       15.78        36.53        20.38        37.25        47.97         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4994 
       57.40        58.98        14.24        53.65        27.22        43.00 
TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5186 
       38.70        37.48        79.30        30.64         9.63        22.78 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4872 
       31.79        23.47        19.82        14.17        75.88        47.18 
TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 
       77.36        57.83        69.86        63.98        68.55        59.44 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5680 TCGA-CJ-5681 
       54.48        38.56         4.57        18.81        25.25        18.15 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-6087 TCGA-CW-6093 
       67.00        62.66        92.02        85.78         1.35       103.43 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5467 TCGA-CZ-5469 
       46.16        60.59        61.41        56.28         2.40        31.10 
TCGA-CZ-5470 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       12.69        65.88        11.67        23.90        18.12         3.91 
TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
        7.96        70.13         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        35.67        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
       19.63        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
       15.75         8.28        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        6.81         0.16        17.49        12.30        86.76        19.27 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95         7.92         2.76       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
       13.78         3.75        14.63         3.02        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       10.68        13.08         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84         6.38        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
       12.92        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           141.73            194.79 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           36.835            26.430 
[1] "0.1 - 141.7 (36.8)" "0.1 - 194.8 (26.4)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED       190       50       115       54
  3P LOSS WILD-TYPE     258       53        75       46
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I               190               258
  STAGE II               50                53
  STAGE III             115                75
  STAGE IV               54                46
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3P LOSS MUTATED   194  62 149   4
  3P LOSS WILD-TYPE 268  61 102  11
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1             194               268
  T2              62                61
  T3             149               102
  T4               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"
                   vv
clus                 N0  N1  N2
  3P LOSS MUTATED   176  18   1
  3P LOSS WILD-TYPE 141  25   5
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             176               141
  N1              18                25
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   316  53
  3P LOSS WILD-TYPE 226  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    316   53
  3P LOSS WILD-TYPE  226   36
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             316               226
  1              53                36
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   133 276
  3P LOSS WILD-TYPE 154 296
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    133  276
  3P LOSS WILD-TYPE  154  296
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             133               154
  MALE               276               296
[1] 2 2
[1] FALSE
D46V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3P LOSS MUTATED                    9                               379
  3P LOSS WILD-TYPE                 57                               145
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3P LOSS MUTATED                                      21
  3P LOSS WILD-TYPE                                   248
D46V9, multiclass
                                       clus
vv                                      3P LOSS MUTATED 3P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                 379               145
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              21               248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V10, continuous
D46V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     6
  3P LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          37   359
  3P LOSS WILD-TYPE                        79   343
D46V12, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          6                 9
  BLACK OR AFRICAN AMERICAN                     37                79
  WHITE                                        359               343
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V13, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    21 269
  3P LOSS WILD-TYPE  21 328
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     21  269
  3P LOSS WILD-TYPE   21  328
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  21                21
  NOT HISPANIC OR LATINO             269               328
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    83  39
  3Q LOSS WILD-TYPE 549 172
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              122               721 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               39               172 
$`3Q LOSS MUTATED`
TCGA-KL-8324 TCGA-KN-8421 TCGA-KN-8425 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8409 
      141.73        87.91       104.52         2.50        42.35        80.38 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3322 
       77.85        57.17        36.82        24.16        49.02        48.59 
TCGA-A3-3324 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3365 TCGA-A3-3372 
       38.99         4.50        52.93        88.37        28.70        24.16 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3433 
       18.64        18.87        20.28         0.10       109.91        72.07 
TCGA-AK-3436 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4811 
       67.20        31.27         1.41         2.53        28.47        46.59 
TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4836 
       52.21        33.50        36.53        14.93        54.48        40.70 
TCGA-B0-5094 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5703 
       10.95        15.95        90.87        26.20        16.21        39.55 
TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-5639 TCGA-B8-4148 TCGA-B8-5163 TCGA-B8-A54I 
       89.49        35.90        32.98        27.16        27.02         4.93 
TCGA-BP-4158 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4329 TCGA-BP-4342 TCGA-BP-4344 
      111.02         0.43        23.05        27.78        74.17        54.77 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4777 
       44.94        31.89        12.33        41.75        13.15        56.91 
TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4977 
       68.38        36.39        36.95         6.71        60.30        14.93 
TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5008 TCGA-BP-5173 
       25.81        16.47        30.64        41.62        35.21         1.78 
TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5195 TCGA-BP-5199 
       74.40        37.22        13.35        27.02        24.62        44.55 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4873 
       34.95        46.55        53.52        11.05        79.66        74.27 
TCGA-CJ-4874 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4900 TCGA-CJ-4904 TCGA-CJ-4907 
       75.06        66.21        51.52        56.35        58.92        49.28 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-4861 
       22.32        61.91        53.26        60.99        83.90        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 
       63.39        93.04         5.46        63.42        58.82        23.74 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5468 
       55.33        55.33        10.85        10.22        21.76         1.94 
TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5907 
       67.96        12.26        14.63        37.15        66.28         4.18 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-2Z-A9JG TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 
        2.01        19.96        54.64         8.88        21.63         4.01 
TCGA-G7-A8LC TCGA-GL-7966 
       17.33         3.68 

$`3Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33       129.37        23.47        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 
       74.93        79.04        92.71        16.67        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
       86.10        61.58        63.95        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 
        0.53        39.16        49.08        37.15        49.58        36.36 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        18.44        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       10.49        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       20.71        28.31        65.52        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       15.78        60.92        68.61        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       22.45        37.58        38.40        28.04        12.13        40.70 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        3.32         1.41         4.57         3.48        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        0.59         5.52        45.07        16.77         6.02        40.44 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       18.51        15.09         8.05         2.24        21.86        52.08 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 
       35.90        11.80        21.60        17.59         1.94        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       90.12        56.94        52.77       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 
       47.97        96.36        61.32        97.41        32.61         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
       12.30        21.30        31.30        11.77        10.36        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67         9.57         5.75         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91        23.74         1.18         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4160 
       17.36        15.42        16.27        14.17        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 
       90.28       101.06        93.34        32.61        99.85        89.36 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
       53.42         3.58        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 
       15.16         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       49.08        12.23        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 
       72.59        77.98        77.62         5.98        44.15        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       13.51        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       20.38        10.98        37.25        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       71.41        63.62        58.68        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        7.23        47.11        53.65        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 
       31.30        36.95        27.22         3.88        46.45         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       43.00        45.07        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       37.48        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 
       74.20        30.64        52.27         9.63        62.86        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5191 
       38.30        42.44        37.25        22.78        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-BP-5202 
       23.47        13.41        33.47        19.82        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       59.84        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 
       54.61        58.95        21.24        83.97        49.25        47.18 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       77.36        64.27        71.87        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       64.18        30.64        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       24.66        27.65        39.45        59.44        50.24        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97        51.29        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
       79.89        84.66        25.71        18.87        25.25        18.15 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       62.10        73.35        67.00        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
      105.93       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-4866 
       47.08        69.21        58.75         6.77        60.59        61.41 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5464 
        0.82        18.44        56.28        56.94        47.01        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       65.65        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       12.16        11.67        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        3.91         6.77         7.96        10.29        70.13        35.87 
TCGA-MM-A563 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.43        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       34.85        56.81        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           141.73            194.79 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            36.46             29.46 
[1] "0.1 - 141.7 (36.5)" "0.1 - 194.8 (29.5)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED        57       21        26       18
  3Q LOSS WILD-TYPE     391       82       164       82
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                57               391
  STAGE II               21                82
  STAGE III              26               164
  STAGE IV               18                82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED    60  25  36   1
  3Q LOSS WILD-TYPE 402  98 215  14
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              60               402
  T2              25                98
  T3              36               215
  T4               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"
                   vv
clus                 N0  N1  N2
  3Q LOSS MUTATED    49   5   1
  3Q LOSS WILD-TYPE 268  38   5
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              49               268
  N1               5                38
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    92  18
  3Q LOSS WILD-TYPE 450  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     92   18
  3Q LOSS WILD-TYPE  450   71
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              92               450
  1              18                71
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    30  92
  3Q LOSS WILD-TYPE 257 480
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     30   92
  3Q LOSS WILD-TYPE  257  480
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              30               257
  MALE                92               480
[1] 2 2
[1] FALSE
D47V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3Q LOSS MUTATED                    8                               108
  3Q LOSS WILD-TYPE                 58                               416
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3Q LOSS MUTATED                                       6
  3Q LOSS WILD-TYPE                                   263
D47V9, multiclass
                                       clus
vv                                      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                 108               416
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               6               263
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V10, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                89 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8428        TCGA-KN-8433        TCGA-KO-8408 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KO-8416        TCGA-A3-A8CQ        TCGA-A3-A8OV        TCGA-A3-A8OW 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-4621        TCGA-B8-5158        TCGA-B8-5164 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B8-A54E        TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-G6-A5PC        TCGA-G6-A8L7        TCGA-MM-A563 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J2        TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JD        TCGA-2Z-A9JI        TCGA-2Z-A9JK        TCGA-2Z-A9JM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-2Z-A9JQ        TCGA-4A-A93W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B1-A654        TCGA-B9-4115        TCGA-B9-4117        TCGA-B9-7268 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-A44B        TCGA-B9-A69E        TCGA-DW-5561        TCGA-DW-7834 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501        TCGA-G7-A8LB 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A59T 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A40U        TCGA-IA-A83S        TCGA-IZ-A6M8        TCGA-MH-A854 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-PJ-A5Z9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-Y8-A894        TCGA-Y8-A896        TCGA-Y8-A8RY 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ 
"3Q LOSS WILD-TYPE" 
D47V11, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                66 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-A3-A8OV 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A3-A8OW        TCGA-B2-A4SR        TCGA-B8-5158        TCGA-DV-A4W0 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G6-A8L7        TCGA-MM-A563        TCGA-MM-A84U        TCGA-2Z-A9J3 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD        TCGA-2Z-A9JI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-A69E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     1
  3Q LOSS WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           7   111
  3Q LOSS WILD-TYPE                       109   591
D47V12, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      7               109
  WHITE                                        111               591
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V13, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     6  74
  3Q LOSS WILD-TYPE  36 523
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   74
  3Q LOSS WILD-TYPE   36  523
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              74               523
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    49  46
  4P LOSS WILD-TYPE 583 165
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               95               748 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               46               165 
$`4P LOSS MUTATED`
TCGA-KN-8427 TCGA-A3-3316 TCGA-A3-3352 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3385 
        0.99        49.08        18.44        53.29        18.64        65.52 
TCGA-AK-3436 TCGA-AK-3458 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       67.20        38.40         1.41        19.73         3.16        43.96 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4844 
       46.59         5.52        40.44        36.53        10.09        10.29 
TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5113 
       65.29        36.85         7.30         8.05        52.08        11.80 
TCGA-B0-5116 TCGA-B0-5399 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4154 
       21.60        21.44         0.53         5.46        23.31        24.66 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4343 
       20.91         1.18         6.38        90.28        32.61        62.86 
TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4762 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 
       31.89        12.33        44.15        13.15        10.82        15.78 
TCGA-BP-4974 TCGA-BP-5173 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4644 
        7.23         1.78        42.44        33.47        19.82        11.05 
TCGA-CJ-4878 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4913 
       71.87        27.65        59.44        51.29        49.28        38.56 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CW-5580 
       84.66        25.71        22.32        53.42        75.58        64.57 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       66.31        83.90        18.77        47.08        69.21         6.77 
TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 
       61.41        55.33        10.85        47.54        31.10         4.18 
TCGA-G6-A8L7 TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B1-7332 
       70.13        51.52        12.82        19.63        49.25         7.33 
TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ 
       10.09        22.92        21.63         2.76        79.86        10.68 
TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y 
       13.08        13.68        16.90         3.68        73.25         2.04 
TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        0.13        42.94         6.61        14.07        18.02 

$`4P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       52.93        45.53        29.92        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 
       43.20        55.76        20.71        18.87        28.31        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       60.92        72.07        68.61        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       22.45        37.58        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        1.41         3.32         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        2.14         6.64         3.25        20.25        15.72         0.59 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 
       52.21        45.07        33.50        16.77         6.02        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 
       27.42        53.88         6.71        56.68        11.64        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07        29.03         2.27        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        29.95        19.30        35.90        26.20 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 
       17.59         1.94        16.21        18.21        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        4.64         0.36         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
       25.05        17.19        25.55        25.91        23.01        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        17.16        16.60        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
       14.17       111.02        85.51        94.72       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        74.17        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4763 
       12.30        72.59        77.98        77.62         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       71.80        48.07        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       13.51        56.91        68.38        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
       58.98        14.24        48.89        49.38        45.50        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       28.87        48.10         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
       31.79        23.47        13.41        24.62        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       47.67        49.97        58.92        49.18        50.33        54.48 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       79.89        18.87        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
       73.35        67.00        53.26        60.99        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
        7.36        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        58.75        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 
       18.44        56.28        56.94        55.33        47.01        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        57.21        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
        3.91         6.77         7.96        10.29        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        15.25        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       75.42        34.85        56.81        54.64        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        19.00        24.89         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       34.82        25.15        25.84         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        99.78        87.22        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.13              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            90.28            194.79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            22.32             30.69 
[1] "0.1 - 90.3 (22.3)"  "0.1 - 194.8 (30.7)"
[1] "hr=" "2.8"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED        25        7        41       21
  4P LOSS WILD-TYPE     423       96       149       79
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                25               423
  STAGE II                7                96
  STAGE III              41               149
  STAGE IV               21                79
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P LOSS MUTATED    27  10  53   5
  4P LOSS WILD-TYPE 435 113 198  10
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              27               435
  T2              10               113
  T3              53               198
  T4               5                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4P LOSS MUTATED    36  13   0
  4P LOSS WILD-TYPE 281  30   6
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              36               281
  N1              13                30
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    61  19
  4P LOSS WILD-TYPE 481  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     61   19
  4P LOSS WILD-TYPE  481   70
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              61               481
  1              19                70
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    40  56
  4P LOSS WILD-TYPE 247 516
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     40   56
  4P LOSS WILD-TYPE  247  516
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              40               247
  MALE                56               516
[1] 2 2
[1] FALSE
D48V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4P LOSS MUTATED                    1                                72
  4P LOSS WILD-TYPE                 65                               452
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4P LOSS MUTATED                                      23
  4P LOSS WILD-TYPE                                   246
D48V9, multiclass
                                       clus
vv                                      4P LOSS MUTATED 4P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  72               452
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              23               246
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V10, continuous
D48V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     3
  4P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           7    80
  4P LOSS WILD-TYPE                       109   622
D48V12, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                      7               109
  WHITE                                         80               622
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V13, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     6  65
  4P LOSS WILD-TYPE  36 532
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   65
  4P LOSS WILD-TYPE   36  532
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              65               532
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    45  44
  4Q LOSS WILD-TYPE 587 167
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               89               754 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               44               167 
$`4Q LOSS MUTATED`
TCGA-KN-8427 TCGA-A3-3316 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3373 TCGA-A3-3380 
        0.99        49.08         4.50        18.44        53.29        18.64 
TCGA-AK-3436 TCGA-AK-3458 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4707 TCGA-B0-4710 
       67.20        38.40         3.32         1.41        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 
       43.96        46.59         5.52        40.44        36.53        10.09 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5098 
       10.29        65.29        36.85         7.30         8.05        52.08 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5158 TCGA-B8-5162 
       11.80        21.60         5.46        23.31        20.91         1.18 
TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4353 
        6.38        90.28        32.61        62.86        31.89        12.33 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4974 TCGA-BP-5173 TCGA-BP-5183 
       13.15        10.82        15.78         7.23         1.78        42.44 
TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4644 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4903 
       33.47        19.82        11.05        66.21        59.44        51.29 
TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5580 
       49.28        84.66        25.71        22.32        53.42        64.57 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       66.31        83.90        18.77        47.08        69.21         6.77 
TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 
       61.41        55.33        10.85        47.54        31.10         4.18 
TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7287 TCGA-A4-A57E TCGA-AL-A5DJ TCGA-B1-7332 
       51.52        12.82        19.63         8.48        49.25         7.33 
TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-F9-A4JJ 
       10.09        19.27        21.63         2.76        79.86        10.68 
TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-A5NK TCGA-IA-A40Y 
       13.08        13.68        16.90         3.68        73.25         2.04 
TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 
        0.13        42.94         6.61        14.07        18.02 

$`4Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
       37.38        48.82        21.86        34.29        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 
       10.49        28.70        74.63        74.76        24.16        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       60.92        72.07        68.61        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       22.45        37.58        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 
        6.64         3.25        20.25        15.72         0.59        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 
       45.07        33.50        16.77         6.02        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        78.44        68.71        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 
       53.88         6.71        56.68        11.64        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 
       11.90        25.32        18.51        15.09        10.95         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 
       30.48        29.95        19.30        35.90        26.20        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         0.36         0.23        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       27.55        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.01        23.74        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       74.17        54.77        49.08        44.94        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       11.64        60.95        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        49.15        38.30        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        53.52        58.95        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       71.87        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        60.99        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
        7.36        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        58.75        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 
       18.44        56.28        56.94        55.33        47.01        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        57.21        22.52         2.40         1.94        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        3.91         6.77         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ 
       67.30        75.42        34.85        56.81        54.64        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       18.21        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       12.46        16.96        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       43.20        47.80        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       25.35        13.25        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        7.92       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        19.00        24.89         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       34.82        25.15        25.84         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       15.48        99.78        87.22        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.13              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            90.28            194.79 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           19.730            31.135 
[1] "0.1 - 90.3 (19.7)"  "0.1 - 194.8 (31.1)"
[1] "hr=" "3"  
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED        20        7        38       23
  4Q LOSS WILD-TYPE     428       96       152       77
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                20               428
  STAGE II                7                96
  STAGE III              38               152
  STAGE IV               23                77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q LOSS MUTATED    22  11  50   6
  4Q LOSS WILD-TYPE 440 112 201   9
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              22               440
  T2              11               112
  T3              50               201
  T4               6                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  4Q LOSS MUTATED    31  12   0
  4Q LOSS WILD-TYPE 286  31   6
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              31               286
  N1              12                31
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    54  21
  4Q LOSS WILD-TYPE 488  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     54   21
  4Q LOSS WILD-TYPE  488   68
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              54               488
  1              21                68
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    33  57
  4Q LOSS WILD-TYPE 254 515
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     33   57
  4Q LOSS WILD-TYPE  254  515
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              33               254
  MALE                57               515
[1] 2 2
[1] FALSE
D49V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4Q LOSS MUTATED                    1                                65
  4Q LOSS WILD-TYPE                 65                               459
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4Q LOSS MUTATED                                      24
  4Q LOSS WILD-TYPE                                   245
D49V9, multiclass
                                       clus
vv                                      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  65               459
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              24               245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V10, continuous
D49V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     3
  4Q LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           6    75
  4Q LOSS WILD-TYPE                       110   627
D49V12, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                      6               110
  WHITE                                         75               627
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V13, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     5  60
  4Q LOSS WILD-TYPE  37 537
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   60
  4Q LOSS WILD-TYPE   37  537
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                37
  NOT HISPANIC OR LATINO              60               537
[1] 2 2
[1] FALSE

Clustering(50) Variable = 5P LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                 0   1
  5P LOSS MUTATED    12  11
  5P LOSS WILD-TYPE 620 200
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               820 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               200 
$`5P LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8442 
      141.73       108.62        24.79        62.37       151.96        47.24 
TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 TCGA-AK-3433 TCGA-B0-4688 TCGA-B0-5107 
       19.33        74.93        80.38        72.07         3.32        30.48 
TCGA-B8-4143 TCGA-BP-4770 TCGA-CJ-4901 TCGA-CZ-5469 TCGA-A4-7286 TCGA-A4-7287 
       23.31        10.82        47.67        31.10        18.21        19.63 
TCGA-BQ-5879 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-G7-6793 TCGA-P4-A5EA 
       22.92         2.76        10.68        11.05         6.61 

$`5P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       28.80        54.74        23.28        44.91        28.80        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        0.23         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
       54.90        97.45        53.42         3.58        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       80.68        37.25        21.21        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 
       44.94        12.23        31.89        11.31        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       52.27         9.63        62.86        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 
       22.49         0.13        12.82        11.57        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 
        0.95        11.97         7.92       123.62        48.26        96.92 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
       93.34        44.84        61.28        50.40        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       20.12        11.28         7.63         7.04         7.17         3.81 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.61        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       13.78         3.75        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       24.89        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        48.62        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.76              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           151.96            194.79 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            24.79             30.61 
[1] "2.8 - 152.0 (24.8)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.8"
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P LOSS MUTATED         2        9         5        7
  5P LOSS WILD-TYPE     446       94       185       93
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 2               446
  STAGE II                9                94
  STAGE III               5               185
  STAGE IV                7                93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5P LOSS MUTATED     2  10  10   2
  5P LOSS WILD-TYPE 460 113 241  13
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               2               460
  T2              10               113
  T3              10               241
  T4               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5P LOSS MUTATED    12   3   2
  5P LOSS WILD-TYPE 305  40   4
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              12               305
  N1               3                40
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    11   4
  5P LOSS WILD-TYPE 531  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     11    4
  5P LOSS WILD-TYPE  531   85
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              11               531
  1               4                85
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    13  11
  5P LOSS WILD-TYPE 274 561
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     13   11
  5P LOSS WILD-TYPE  274  561
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              13               274
  MALE                11               561
[1] 2 2
[1] FALSE
D50V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5P LOSS MUTATED                   10                                 7
  5P LOSS WILD-TYPE                 56                               517
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5P LOSS MUTATED                                       7
  5P LOSS WILD-TYPE                                   262
D50V9, multiclass
                                       clus
vv                                      5P LOSS MUTATED 5P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                   7               517
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V10, continuous
D50V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     1
  5P LOSS WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           2    18
  5P LOSS WILD-TYPE                       114   684
D50V12, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      2               114
  WHITE                                         18               684
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V13, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  14
  5P LOSS WILD-TYPE  39 583
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   14
  5P LOSS WILD-TYPE   39  583
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              14               583
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    13   8
  5Q LOSS WILD-TYPE 619 203
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               21               822 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8               203 
$`5Q LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8442 
      141.73       108.62        24.79        62.37       151.96        47.24 
TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 TCGA-AK-3433 TCGA-B0-4688 TCGA-BP-4770 
       19.33        74.93        80.38        72.07         3.32        10.82 
TCGA-CJ-4901 TCGA-CZ-5469 TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5879 TCGA-BQ-5894 
       47.67        31.10        18.21        19.63        22.92         2.76 
TCGA-F9-A4JJ TCGA-GL-7966 TCGA-P4-A5EA 
       10.68         3.68         6.61 

$`5Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07        23.84       109.22       137.06       102.81        90.48 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        28.11        66.54        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8443 
       28.80        54.74        23.28        44.91        28.80        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        10.68        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       73.08        66.31        15.78        60.92        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       31.27        28.04        12.13        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       13.15        61.68         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        56.35        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        63.72        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 
       10.88         7.66         0.95        11.97         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       34.19        19.00        24.89        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.33        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.76              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           151.96            194.79 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            24.79             30.53 
[1] "2.8 - 152.0 (24.8)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1.4"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         2        9         6        4
  5Q LOSS WILD-TYPE     446       94       184       96
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 2               446
  STAGE II                9                94
  STAGE III               6               184
  STAGE IV                4                96
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  5Q LOSS MUTATED     2   9   9   2
  5Q LOSS WILD-TYPE 460 114 242  13
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               2               460
  T2               9               114
  T3               9               242
  T4               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  5Q LOSS MUTATED    10   4   1
  5Q LOSS WILD-TYPE 307  39   5
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              10               307
  N1               4                39
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    11   2
  5Q LOSS WILD-TYPE 531  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11    2
  5Q LOSS WILD-TYPE  531   87
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              11               531
  1               2                87
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    11  11
  5Q LOSS WILD-TYPE 276 561
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   11
  5Q LOSS WILD-TYPE  276  561
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              11               276
  MALE                11               561
[1] 2 2
[1] FALSE
D51V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5Q LOSS MUTATED                   10                                 5
  5Q LOSS WILD-TYPE                 56                               519
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5Q LOSS MUTATED                                       7
  5Q LOSS WILD-TYPE                                   262
D51V9, multiclass
                                       clus
vv                                      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                   5               519
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V10, continuous
D51V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     1
  5Q LOSS WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           2    16
  5Q LOSS WILD-TYPE                       114   686
D51V12, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                14
  BLACK OR AFRICAN AMERICAN                      2               114
  WHITE                                         16               686
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V13, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3  12
  5Q LOSS WILD-TYPE  39 585
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   12
  5Q LOSS WILD-TYPE   39  585
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              12               585
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   121  47
  6P LOSS WILD-TYPE 511 164
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              168               675 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               47               164 
$`6P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       52.27        87.12        19.33         2.50        59.08       115.00 
TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       16.67        80.38       103.27        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3335 TCGA-A3-3336 
       63.95        36.82        49.08        37.15        21.86        34.29 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 
        4.50        52.93        18.44        43.20        18.64        18.87 
TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       29.10        15.78        72.07        68.61        67.20        57.37 
TCGA-AK-3447 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 
       40.01        38.40        12.13        40.70         1.41         3.48 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4813 
       28.47         1.38         3.62        19.73        43.96         0.59 
TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-5084 
       36.53        54.48        10.09        40.70        10.29         7.30 
TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 TCGA-B4-5377 TCGA-B4-5832 
       29.95        17.59        52.77        32.61         9.57         0.23 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5158 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 
        5.46        25.55        20.91        32.61        89.36        64.27 
TCGA-BP-4327 TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 
        3.58        21.21        74.17        11.31        12.33         5.98 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 
       13.15        10.82        60.59        15.78        36.39        87.45 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       71.41        58.68        57.40        46.45        31.30        25.81 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 
       16.47        43.00         6.35        30.64        62.86        74.40 
TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4872 
       37.22        31.79        31.27        46.55        79.66        47.18 
TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 TCGA-CJ-4907 
       66.21        30.64        59.44        47.67        58.92        49.28 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4853 
       84.66        22.32        60.99        53.42        66.31        25.45 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5465 TCGA-CZ-5468 
       69.21        61.41        58.82        56.28        47.54         1.94 
TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-5568 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-MM-A563 
       67.96        14.63        12.16         4.18        70.13        19.43 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5882 TCGA-BQ-7056 
       54.64        51.52        18.21        10.09        21.63        20.12 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7502 
       19.00        13.08         4.01        11.05        25.15        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5E8 TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-Y8-A896 
       17.33         3.68        42.94        27.06        18.02        18.64 

$`6P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.06        31.33        23.47        25.91         3.55         0.99 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
       11.21       100.87        87.78        86.10        12.66        12.16 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 
       47.21         0.53        39.16        24.16        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       31.07        45.53        29.92        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       53.29        55.76        20.71        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 
      109.91        84.36        73.08        66.31        60.92        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       22.45        37.58        31.27        28.04         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        4.57         2.53        19.00        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14         3.16         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
        6.02        40.44        14.93        29.10        78.44        68.71 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
       56.78        60.33        84.92        90.12        56.94        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       61.32        97.41        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         1.25         0.53         4.64         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       17.19        25.91        23.01        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       93.34        99.85         0.43        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       61.78        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       31.89        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.62        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       60.95        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4963 
       36.95         6.71        47.97         6.94        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51         6.74        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        36.95        27.22         3.88        46.45 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       48.10        79.30         1.78        74.20        52.27         9.63 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       27.02        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
       19.82        44.55        34.95         0.95        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 
       58.95        11.05        21.24        83.97        49.25        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       69.86        64.18        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       49.97        51.29        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       79.89        25.71        18.87        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 
       62.10        73.35        67.00        53.26        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        46.16         0.59        47.08 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
        5.46        63.42         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       57.21        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       65.65        12.26        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       65.88        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.02        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
       35.87         2.01        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       67.30        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       50.40        49.84        26.27        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       34.19        24.89        10.68         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM 
       51.78        48.62        39.25        34.82        13.68         6.38 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       17.98        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
       47.90        47.44        33.04        28.80        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       29.00        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.23              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           151.96            194.79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            40.70             28.73 
[1] "0.2 - 152.0 (40.7)" "0.1 - 194.8 (28.7)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        59       36        47       27
  6P LOSS WILD-TYPE     389       67       143       73
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                59               389
  STAGE II               36                67
  STAGE III              47               143
  STAGE IV               27                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6P LOSS MUTATED    60  39  66   5
  6P LOSS WILD-TYPE 402  84 185  10
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              60               402
  T2              39                84
  T3              66               185
  T4               5                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6P LOSS MUTATED    72  12   4
  6P LOSS WILD-TYPE 245  31   2
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              72               245
  N1              12                31
  N2               4                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V6, binary
                   cls
clus                  0   1
  6P LOSS MUTATED   116  20
  6P LOSS WILD-TYPE 426  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    116   20
  6P LOSS WILD-TYPE  426   69
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0             116               426
  1              20                69
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    53 117
  6P LOSS WILD-TYPE 234 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     53  117
  6P LOSS WILD-TYPE  234  455
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              53               234
  MALE               117               455
[1] 2 2
[1] FALSE
D52V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6P LOSS MUTATED                   50                               101
  6P LOSS WILD-TYPE                 16                               423
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6P LOSS MUTATED                                      19
  6P LOSS WILD-TYPE                                   250
D52V9, multiclass
                                       clus
vv                                      6P LOSS MUTATED 6P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 50                16
  KIDNEY CLEAR CELL RENAL CARCINOMA                 101               423
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              19               250
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V10, continuous
D52V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     4
  6P LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           8   151
  6P LOSS WILD-TYPE                       108   551
D52V12, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                11
  BLACK OR AFRICAN AMERICAN                      8               108
  WHITE                                        151               551
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V13, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     8 102
  6P LOSS WILD-TYPE  34 495
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8  102
  6P LOSS WILD-TYPE   34  495
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                34
  NOT HISPANIC OR LATINO             102               495
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   154  48
  6Q LOSS WILD-TYPE 478 163
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              202               641 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               48               163 
$`6Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       73.91        54.74       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 
       92.71        16.67        80.38       103.27        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       61.58        63.95        36.82        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 
       49.58        21.86        34.29         4.50        52.93        18.44 
TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 
       43.20        18.64        18.87         0.10        29.10        15.78 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 
       72.07        68.61        67.20        57.37        40.01        38.40 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 
       12.13        40.70         1.41         3.48        28.47         1.38 
TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4810 TCGA-B0-4822 TCGA-B0-4824 
        3.62        19.73        43.96        15.72        36.53        54.48 
TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4849 TCGA-B0-5084 TCGA-B0-5108 
       10.09        40.70        10.29         2.27         7.30        29.95 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 
       17.59         1.94        14.76        52.77        32.61        21.57 
TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4148 TCGA-B8-4620 
        9.57         0.23         0.53         5.46        27.16        25.55 
TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 
       20.91         1.74        32.61        89.36        64.27        97.45 
TCGA-BP-4327 TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4761 
        3.58        21.21        74.17        11.31        12.33         5.98 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4787 TCGA-BP-4797 
       13.15        10.82        60.59        56.91        15.78        36.39 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 
       87.45        71.41        58.68        60.30        57.40        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5000 
       31.30        25.81        36.95        16.47        43.00        18.51 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5191 
        6.35        30.64        62.86        74.40        37.22        31.79 
TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 
       31.27        59.84        46.55        58.95        79.66        47.18 
TCGA-CJ-4881 TCGA-CJ-4887 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4901 
       66.21        30.64        24.66        39.45        59.44        47.67 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6027 
       58.92        49.28        79.89        84.66        22.32        60.99 
TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4853 
       53.42        83.77         5.39        85.78        66.31        25.45 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 
       69.21        58.75        61.41        58.82        56.28        47.01 
TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-5568 TCGA-DV-5573 
       47.54        80.19        67.96        14.63        12.16        37.15 
TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 
       56.84         4.18        70.13        19.43        10.85        67.30 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B 
       54.64        51.52        35.67        18.21        10.09         2.10 
TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5888 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 
       86.76        21.63        13.25        20.12        19.00        13.08 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 
        4.01        11.05        25.84        17.33         3.68         0.13 
TCGA-P4-A5EB TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-Y8-A896 
       84.95        27.06        18.02        18.64 

$`6Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 
      109.22        71.41        28.80        62.37        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
      100.87        87.78        86.10        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        0.53        39.16        24.16        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       24.69        37.38        48.82        31.07        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        24.16        53.29        55.76        20.71 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62       109.91        84.36        73.08        66.31 
TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       60.92        46.78        48.36        42.08        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       45.93        28.73        22.45        37.58        31.27        28.04 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 
        1.41         3.32         4.57         2.53        19.00        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14         3.16         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       20.25        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 
       33.50        16.77         6.02        40.44        14.93        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        11.64        65.29        39.45        26.07        29.03 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
       21.60        16.21        18.21        21.44        37.22        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 
       60.33        84.92        90.12        56.94        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 
       11.77        10.36        32.98        16.67         5.75         1.25 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 
        4.64         0.36         0.23        23.31        16.80        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
       25.05        24.66        17.19        25.91        23.01        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       29.88        17.06         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        54.90        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       80.68        37.25        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       31.89        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.62        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        5.33        61.97        13.51        68.38        11.64        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 
        6.71        47.97         6.94        63.62        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
       27.22         3.88        46.45         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        49.15        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       22.78        13.35        27.02        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
       24.62        33.47        19.82        44.55        34.95         0.95 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 
       53.52        11.05        21.24        83.97        49.25        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        77.36        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       69.86        64.18        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       50.01        27.65        50.24        56.35        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57        18.81        63.88        72.00        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.26        75.58        62.66         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       81.83        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        18.77        46.16         0.59        47.08 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
        6.77        14.66        60.59        63.39        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       63.42         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        10.85        10.22        21.76        57.21        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40         1.94        31.10        12.69        65.65        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        65.88        11.67 
TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        23.90        66.02        18.12         3.91         6.77 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U 
        7.96        10.29        35.87         2.01        19.96        15.25 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL 
        4.57        75.42        34.85        56.81        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       26.04        25.35        10.88         7.66         0.95        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 
       44.84        61.28        50.40        49.84        26.27        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       61.02        54.90        34.19        24.89        10.68         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        1.18         0.43        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       12.99        26.01        29.00        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           151.96            194.79 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           40.355            28.180 
[1] "0.1 - 152.0 (40.4)" "0.1 - 194.8 (28.2)"
[1] "hr=" "1.3"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        82       40        50       31
  6Q LOSS WILD-TYPE     366       63       140       69
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                82               366
  STAGE II               40                63
  STAGE III              50               140
  STAGE IV               31                69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  6Q LOSS MUTATED    82  42  73   7
  6Q LOSS WILD-TYPE 380  81 178   8
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              82               380
  T2              42                81
  T3              73               178
  T4               7                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  6Q LOSS MUTATED    82  15   4
  6Q LOSS WILD-TYPE 235  28   2
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              82               235
  N1              15                28
  N2               4                 2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   142  22
  6Q LOSS WILD-TYPE 400  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    142   22
  6Q LOSS WILD-TYPE  400   67
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             142               400
  1              22                67
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    72 132
  6Q LOSS WILD-TYPE 215 440
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     72  132
  6Q LOSS WILD-TYPE  215  440
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              72               215
  MALE               132               440
[1] 2 2
[1] FALSE
D53V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6Q LOSS MUTATED                   51                               129
  6Q LOSS WILD-TYPE                 15                               395
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6Q LOSS MUTATED                                      24
  6Q LOSS WILD-TYPE                                   245
D53V9, multiclass
                                       clus
vv                                      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 51                15
  KIDNEY CLEAR CELL RENAL CARCINOMA                 129               395
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              24               245
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V10, continuous
D53V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     6
  6Q LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          12   178
  6Q LOSS WILD-TYPE                       104   524
D53V12, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          6                 9
  BLACK OR AFRICAN AMERICAN                     12               104
  WHITE                                        178               524
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V13, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    11 123
  6Q LOSS WILD-TYPE  31 474
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11  123
  6Q LOSS WILD-TYPE   31  474
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             123               474
[1] 2 2
[1] FALSE

Clustering(54) Variable = 7P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                 0   1
  7P LOSS MUTATED     2   2
  7P LOSS WILD-TYPE 630 209
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               839 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               209 
$`7P LOSS MUTATED`
TCGA-KL-8332 TCGA-B0-4698 TCGA-BP-4761 TCGA-A4-A5Y1 
       84.89         1.38         5.98        12.99 

$`7P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       72.07        68.61        67.20        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       66.02        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       56.81        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             1.38              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            84.89            194.79 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            9.485            30.580 
[1] "1.4 - 84.9 (9.5)"   "0.1 - 194.8 (30.6)"
[1] "hr=" "3"  
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         1        0         2        1
  7P LOSS WILD-TYPE     447      103       188       99
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1               447
  STAGE II                0               103
  STAGE III               2               188
  STAGE IV                1                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7P LOSS MUTATED     2   0   1   1
  7P LOSS WILD-TYPE 460 123 250  14
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               2               460
  T2               0               123
  T3               1               250
  T4               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"
                   vv
clus                 N0  N1  N2
  7P LOSS MUTATED     1   2   0
  7P LOSS WILD-TYPE 316  41   6
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               1               316
  N1               2                41
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 539  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE  539   89
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               3               539
  1               0                89
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   4
  7P LOSS WILD-TYPE 287 568
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    4
  7P LOSS WILD-TYPE  287  568
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0               287
  MALE                 4               568
[1] 2 2
[1] FALSE
D54V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7P LOSS MUTATED                    1                                 2
  7P LOSS WILD-TYPE                 65                               522
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7P LOSS MUTATED                                       1
  7P LOSS WILD-TYPE                                   268
D54V9, multiclass
                                       clus
vv                                      7P LOSS MUTATED 7P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               522
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V10, continuous
D54V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0     4
  7P LOSS WILD-TYPE                       116   698
D54V12, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                15
  BLACK OR AFRICAN AMERICAN                      0               116
  WHITE                                          4               698
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V13, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE  42 595
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   42  595
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO               2               595
[1] 2 2
[1] FALSE

Clustering(55) Variable = 7Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     2   2
  7Q LOSS WILD-TYPE 630 209
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               839 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               209 
$`7Q LOSS MUTATED`
TCGA-KL-8332 TCGA-B0-4698 TCGA-BP-4761 TCGA-A4-A5Y1 
       84.89         1.38         5.98        12.99 

$`7Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 
       30.25        44.84        86.56        28.11        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       72.07        68.61        67.20        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98        77.62        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        57.21        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       66.02        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
       10.29        70.13        35.87         2.01        19.43        19.96 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       56.81        54.64        51.52        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 
       16.18        22.49         0.13        12.82        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             1.38              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            84.89            194.79 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            9.485            30.580 
[1] "1.4 - 84.9 (9.5)"   "0.1 - 194.8 (30.6)"
[1] "hr=" "3"  
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        0         2        1
  7Q LOSS WILD-TYPE     447      103       188       99
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1               447
  STAGE II                0               103
  STAGE III               2               188
  STAGE IV                1                99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     2   0   1   1
  7Q LOSS WILD-TYPE 460 123 250  14
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               2               460
  T2               0               123
  T3               1               250
  T4               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"
                   vv
clus                 N0  N1  N2
  7Q LOSS MUTATED     1   2   0
  7Q LOSS WILD-TYPE 316  41   6
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               1               316
  N1               2                41
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 539  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    0
  7Q LOSS WILD-TYPE  539   89
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               3               539
  1               0                89
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   4
  7Q LOSS WILD-TYPE 287 568
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    4
  7Q LOSS WILD-TYPE  287  568
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0               287
  MALE                 4               568
[1] 2 2
[1] FALSE
D55V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7Q LOSS MUTATED                    1                                 2
  7Q LOSS WILD-TYPE                 65                               522
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7Q LOSS MUTATED                                       1
  7Q LOSS WILD-TYPE                                   268
D55V9, multiclass
                                       clus
vv                                      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               522
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V10, continuous
D55V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           0     4
  7Q LOSS WILD-TYPE                       116   698
D55V12, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                15
  BLACK OR AFRICAN AMERICAN                      0               116
  WHITE                                          4               698
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V13, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   2
  7Q LOSS WILD-TYPE  42 595
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    2
  7Q LOSS WILD-TYPE   42  595
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO               2               595
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   107  54
  8P LOSS WILD-TYPE 525 157
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               682 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               54               157 
$`8P LOSS MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 
      137.06        44.84       123.12         2.50       115.00        42.35 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3319 TCGA-A3-3325 
      103.27        77.85        61.58        63.95        37.15        24.69 
TCGA-A3-3336 TCGA-A3-3346 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3382 
       34.29         4.50        28.70        24.16        53.29        18.87 
TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
        0.10       109.91        29.10        68.61        67.20        57.37 
TCGA-AK-3447 TCGA-AK-3458 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4699 
       40.01        38.40        40.70         3.32        28.47         3.62 
TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4815 
        5.98        19.73        43.96        20.25         0.59        52.21 
TCGA-B0-4816 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4838 
       45.07         6.02        40.44        36.53        40.70        27.42 
TCGA-B0-4845 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5094 TCGA-B0-5102 TCGA-B0-5108 
       65.29         2.27        70.52        10.95        90.87        29.95 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-A4SR TCGA-B4-5377 
       46.68        56.78        89.49        61.32        16.67         9.57 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-5158 TCGA-B8-5163 
        5.46        23.31        27.16        27.55        20.91        27.02 
TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4164 
        0.85        17.16         6.38         0.53         4.93        32.61 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4338 TCGA-BP-4340 
       61.78        64.27        53.42         3.58        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       52.24        62.86        44.94        31.89        11.31        12.33 
TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4799 
       60.59        68.38        11.64        15.78        10.98        37.25 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        6.94        87.45        71.41        61.51         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4998 
       14.24        45.50        46.45        25.81        43.00        30.64 
TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5200 
       37.02         1.78        30.64         9.63        38.30        34.95 
TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 
       31.27        65.69        53.52        58.95        21.24        49.25 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4888 
       64.27        71.87        66.21        57.83        69.86        51.52 
TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 
       63.98        27.65        59.44        51.29        58.92        49.28 
TCGA-CJ-4912 TCGA-CJ-5672 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6027 
       54.48        72.00        25.71        22.32        53.26        60.99 
TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4860 
       75.58         7.36       105.93        83.90        46.16         6.77 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5463 
       60.59         5.46         0.82        55.33        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 
       47.54        22.52         1.94        12.26        22.78        43.69 
TCGA-DV-5574 TCGA-DV-5575 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-2Z-A9J3 TCGA-A4-A5Y1 
       66.28        56.84        35.87        19.43        58.22        12.99 
TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 TCGA-DW-5560 TCGA-F9-A7Q0 
        9.63         7.33        10.09        10.88        11.61        13.08 
TCGA-F9-A8NY TCGA-G7-A8LC TCGA-G7-A8LD TCGA-SX-A7SO TCGA-UN-AAZ9 
        1.18        17.33        16.90        38.63        18.02 

$`8P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24        49.97        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       11.21        59.08       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       79.04        92.71        16.67        80.38        87.78        86.10 
TCGA-KO-8415 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       57.17        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
       39.16        24.16        49.08        49.02        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 
       36.36        38.99        37.38        48.82        21.86        31.07 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 
       82.32        51.25        10.49        74.63        74.76        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.64        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 
       15.39        22.65         0.10        11.18        10.62        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 
       73.08        66.31        15.78        60.92        72.07        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       48.36        42.08        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 
       22.45        37.58        31.27        28.04        12.13         1.41 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
       65.10         7.82         2.14         3.16         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 
       15.72        46.59         5.52        33.50        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        68.71        45.30 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        11.64        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       26.07        29.03        36.85        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 
       11.90         7.30        25.32        18.51        15.09         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        2.24        21.86        52.08        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       15.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 
       31.30        11.77        10.36        32.98        21.57         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        0.23         1.25         0.53         4.64         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
       16.80        25.05        24.66        17.19        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 
       23.01        23.74         1.18        24.23        16.60        14.27 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        8.42        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 
        0.43        89.36        23.05        77.03        62.24        54.90 
TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
       97.45        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 
       15.16         0.07        74.17        54.77        49.08        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       61.68        10.82         5.33        61.97        13.51        56.91 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
       60.95        48.95        36.53        20.38        36.39        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.71        47.97        63.62        58.68        60.30        61.22 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       58.98        48.89        49.38         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 
       14.93        36.07        33.34        31.30        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
        3.88        46.45        16.47         5.82        45.07        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       18.51        38.70        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       28.87        48.10         6.35        79.30        74.20        52.27 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        49.15        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        44.55         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       54.61        11.05        83.97        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4890 
       75.06        77.36        61.91        64.18        30.64        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
       47.67        49.97        49.18        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        3.06         4.57        18.81        63.88        79.89        84.66 
TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
       67.00        53.42        62.66        83.77        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       81.83         5.39        85.78        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 
       74.66         1.35       103.43        18.77        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       47.08        69.21        58.75        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       61.41        63.42        58.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5467 
       56.94        55.33        47.01        10.85        57.21         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
       31.10        12.69        80.19        67.96        65.65        14.63 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       62.63        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U 
        7.96        10.29        70.13         2.01        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       10.85         7.04        75.55        59.01       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
        8.48        16.31        15.75         8.28        12.46        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         7.17         3.81        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       54.90        34.19        19.00        24.89        10.68         2.40 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.10              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           137.06            194.79 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
            36.53             29.41 
[1] "0.1 - 137.1 (36.5)" "0.1 - 194.8 (29.4)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED        70       21        43       27
  8P LOSS WILD-TYPE     378       82       147       73
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                70               378
  STAGE II               21                82
  STAGE III              43               147
  STAGE IV               27                73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8P LOSS MUTATED    72  23  62   4
  8P LOSS WILD-TYPE 390 100 189  11
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              72               390
  T2              23               100
  T3              62               189
  T4               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"
                   vv
clus                 N0  N1  N2
  8P LOSS MUTATED    61  10   0
  8P LOSS WILD-TYPE 256  33   6
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              61               256
  N1              10                33
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   119  28
  8P LOSS WILD-TYPE 423  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    119   28
  8P LOSS WILD-TYPE  423   61
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             119               423
  1              28                61
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    50 111
  8P LOSS WILD-TYPE 237 461
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     50  111
  8P LOSS WILD-TYPE  237  461
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              50               237
  MALE               111               461
[1] 2 2
[1] FALSE
D56V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8P LOSS MUTATED                   10                               138
  8P LOSS WILD-TYPE                 56                               386
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8P LOSS MUTATED                                      13
  8P LOSS WILD-TYPE                                   256
D56V9, multiclass
                                       clus
vv                                      8P LOSS MUTATED 8P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                 138               386
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              13               256
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V10, continuous
D56V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     6
  8P LOSS WILD-TYPE                                2     9
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          12   141
  8P LOSS WILD-TYPE                       104   561
D56V12, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          6                 9
  BLACK OR AFRICAN AMERICAN                     12               104
  WHITE                                        141               561
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V13, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11 103
  8P LOSS WILD-TYPE  31 494
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11  103
  8P LOSS WILD-TYPE   31  494
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             103               494
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    63  22
  8Q LOSS WILD-TYPE 569 189
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               85               758 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               189 
$`8Q LOSS MUTATED`
TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8436 TCGA-KO-8411 
      137.06        44.84       123.12         2.50        42.35       103.27 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3325 TCGA-A3-3365 TCGA-A3-3372 
       77.85        61.58        63.95        24.69        28.70        24.16 
TCGA-A3-3373 TCGA-A3-A6NN TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3440 TCGA-AK-3458 
       53.29         0.10       109.91        29.10        57.37        38.40 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4821 
       40.70         3.32         3.62        20.25         0.59        40.44 
TCGA-B0-4822 TCGA-B0-4845 TCGA-B0-4945 TCGA-B0-5696 TCGA-B4-5838 TCGA-B8-5164 
       36.53        65.29        70.52        56.78         5.46         0.85 
TCGA-B8-5545 TCGA-B8-5549 TCGA-BP-4174 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4347 
       17.16         6.38        61.78        18.48        62.86        44.94 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4787 
       31.89        11.31        12.33        60.59        68.38        15.78 
TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5004 
       71.41         6.74        57.40        45.50        43.00        37.02 
TCGA-BP-5177 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4876 
        9.63        34.95        31.27        65.69        53.52        64.27 
TCGA-CJ-4885 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 
       69.86        51.52        63.98        27.65        59.44        51.29 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6088 
       58.92        49.28        22.32        53.26        75.58       105.93 
TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 
       83.90         6.77        60.59         0.82        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5575 TCGA-MM-A563 
       21.76        47.54        12.26        22.78        56.84        19.43 
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 TCGA-F9-A7Q0 TCGA-G7-A8LC 
       12.99         7.33        10.09        10.88        13.08        17.33 
TCGA-UN-AAZ9 
       18.02 

$`8Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
       44.91        28.80        47.24        49.97        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87        76.90        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
       74.93        79.04        92.71        16.67        80.38        87.78 
TCGA-KO-8413 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       86.10        57.17        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       10.49        74.63        74.76        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 
       22.65         0.10        11.18        10.62        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       45.93        28.73        22.45        37.58        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77         6.02        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        10.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        36.85        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5697 
      112.80        48.89       101.13        15.78        46.68        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       31.30        11.77        10.36        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5546 
       20.91        23.74         1.18        27.02        24.23        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       23.05        77.03        62.24        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4342 
       21.21        15.16         0.07        93.99        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       54.77        49.08        12.23        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       61.97        13.51        56.91        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22        61.51        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       49.38         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       74.20        30.64        52.27        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        44.55         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 
       63.25        73.22        14.17        75.88        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       74.27        75.06        77.36        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       57.83        64.18        30.64        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.18        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       73.35        67.00        60.99        53.42        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6093 
       73.18        66.31        78.18        74.66         1.35       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       63.42        58.82        23.74        18.44        56.28        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        47.01        10.85        57.21        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       14.63        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       11.67        37.15        66.28        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
       35.87         2.01        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        2.20        19.56        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       25.35        13.25         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM 
       41.62        26.47        48.30        43.76        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.10              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           137.06            194.79 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           40.440            29.935 
[1] "0.1 - 137.1 (40.4)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1"  
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED        38       13        22       12
  8Q LOSS WILD-TYPE     410       90       168       88
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                38               410
  STAGE II               13                90
  STAGE III              22               168
  STAGE IV               12                88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED    39  13  30   3
  8Q LOSS WILD-TYPE 423 110 221  12
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              39               423
  T2              13               110
  T3              30               221
  T4               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"
                   vv
clus                 N0  N1  N2
  8Q LOSS MUTATED    34   5   0
  8Q LOSS WILD-TYPE 283  38   6
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              34               283
  N1               5                38
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    64  12
  8Q LOSS WILD-TYPE 478  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     64   12
  8Q LOSS WILD-TYPE  478   77
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              64               478
  1              12                77
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    22  63
  8Q LOSS WILD-TYPE 265 509
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     22   63
  8Q LOSS WILD-TYPE  265  509
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              22               265
  MALE                63               509
[1] 2 2
[1] FALSE
D57V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8Q LOSS MUTATED                    9                                69
  8Q LOSS WILD-TYPE                 57                               455
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8Q LOSS MUTATED                                       7
  8Q LOSS WILD-TYPE                                   262
D57V9, multiclass
                                       clus
vv                                      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  69               455
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V10, continuous
D57V11, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                66 
       TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341        TCGA-KL-8345 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-KO-8409 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-B2-A4SR        TCGA-B8-5158 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-2Z-A9J3 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JD        TCGA-2Z-A9JI 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4117        TCGA-B9-A69E 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-7501 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-GL-A9DD        TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-MH-A856        TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-PJ-A5Z9 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U        TCGA-SX-A7SL 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS        TCGA-UZ-A9PM 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-WN-A9G9        TCGA-WN-AB4C        TCGA-Y8-A894        TCGA-Y8-A896 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RY        TCGA-Y8-A8RZ 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     2
  8Q LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           6    76
  8Q LOSS WILD-TYPE                       110   626
D57V12, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                13
  BLACK OR AFRICAN AMERICAN                      6               110
  WHITE                                         76               626
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V13, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  52
  8Q LOSS WILD-TYPE  36 545
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   52
  8Q LOSS WILD-TYPE   36  545
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              52               545
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   105  83
  9P LOSS WILD-TYPE 527 128
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              188               655 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               83               128 
$`9P LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8427 
      141.73        23.84        84.89        71.41        62.37         0.99 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 
       42.35        10.68        57.17        36.82        39.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 
       49.02        37.15        24.69         4.50        52.93        18.44 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 
       24.16        18.87       109.91        29.10        67.20        42.08 
TCGA-AK-3450 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       58.49        40.70         3.32         1.41         4.57         3.48 
TCGA-B0-4698 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4815 
        1.38        19.73         3.16        43.96        46.59        52.21 
TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 
       33.50         6.02        40.44        36.53        10.09        40.70 
TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       56.68        65.29        29.03        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5113 TCGA-B0-5116 
       21.86        52.08        62.89        30.48        11.80        21.60 
TCGA-B0-5121 TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 
       18.21        14.76        15.78        56.94        11.77        21.57 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 
        0.23         5.46        25.55        23.01        20.91         6.38 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4342 
        0.53        90.28        32.61        89.36        64.27        74.17 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4763 TCGA-BP-4766 
       62.86        31.89        11.31        12.33        41.75        48.07 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 
       13.15        68.38        11.64        36.39        10.98         6.71 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4985 
       71.41        58.68        60.30        61.22        45.50        31.30 
TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5010 
       25.81        43.00        45.07        18.51        36.23        28.87 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 
        6.35        30.64        62.86        74.40        42.44        27.02 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4638 
       31.79        33.47        19.82        31.27        46.55        14.17 
TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 
       79.66        66.21        51.52        68.55        26.93        39.45 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       56.35        47.67        49.28        50.33        54.48        38.56 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 
        4.57        63.88        84.66        25.71        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       61.91        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 
        7.36        64.57         5.39        66.31        83.90        18.77 
TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5461 
       46.16        47.08        69.21         6.77        56.28        10.85 
TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 
       10.22        47.54        22.52        31.10        67.96        65.65 
TCGA-CZ-5987 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A5PC TCGA-G6-A8L7 TCGA-MM-A563 
       14.63        23.90        66.02         7.96        70.13        19.43 
TCGA-MM-A84U TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-4A-A93X TCGA-A4-7286 
       15.25        54.64        51.52        35.67        12.82        18.21 
TCGA-A4-7287 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B3-3926 
       19.63         8.48        12.99         9.63        49.25        10.09 
TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-7048 
       20.61        14.86        22.92        13.25        10.88        93.34 
TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 
       20.12        79.86        13.08         4.01        11.05        34.82 
TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-UN-AAZ9 
       13.68        17.33        16.90         2.04         0.13        18.02 
TCGA-UZ-A9PQ TCGA-Y8-A896 
       86.27        18.64 

$`9P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.22       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.56        28.11        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 
       61.58        63.95        12.66        12.16        47.21         0.53 
TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       24.16        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
       48.82        21.86        34.29        31.07        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       88.37        42.97        82.32        51.25        10.49        28.70 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.63        74.76        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.64        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 
        0.10         0.10        11.18        10.62        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       66.31        15.78        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       46.78        48.36        40.01        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 TCGA-B0-4700 
        1.41         2.53        28.47        19.00         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 
       15.72         0.59         5.52        45.07        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
       53.88         6.71        11.64        10.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 
       11.90         7.30        25.32        18.51        15.09        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 
       26.20        17.59         1.94        16.21        21.44        37.22 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
       79.17       112.80        48.89       101.13        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       60.33        84.92        90.12        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        10.36        32.98        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       17.16        16.60        14.27        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4769 
       77.98        77.62         5.98        44.15        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 
       60.95        15.78        48.95        36.53        20.38        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 
       36.95        47.97         6.94        87.45        63.62        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        5.82        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        48.10        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        49.15        38.30        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95        59.84        63.25        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        83.97        49.25        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       77.36        64.27        71.87        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       64.18        30.64        63.98        50.01        24.66        27.65 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       59.44        50.24        49.97        51.29        58.92        49.18 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 
       45.14         3.06        18.81        72.00        79.89        18.87 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 
       18.15        62.10        73.35        67.00        83.77        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 
      105.93       103.43        25.45         0.59        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5468 
       55.33        47.01        21.76        57.21         2.40         1.94 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       12.69        80.19        12.26        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
       56.84        18.12         3.91         6.77         4.18        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       35.87         2.01        19.96        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       75.42        34.85        56.81        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       22.49         0.13        11.57        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.73        14.33        12.46        16.96        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       25.08        44.61         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       28.18        26.40         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH 
       22.06         2.10        19.23         6.81         0.16        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 
       12.30        86.76        19.27         8.88        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
       47.80        21.63        40.83        26.04        30.28        26.04 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
      123.62        48.26        96.92        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       49.84        26.27        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       24.89        10.68         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       48.62        39.25        25.15        25.84         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       16.31        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.13              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           141.73            194.79 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           31.285            30.280 
[1] "0.1 - 141.7 (31.3)" "0.1 - 194.8 (30.3)"
[1] "hr=" "2.4"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED        65       15        66       42
  9P LOSS WILD-TYPE     383       88       124       58
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                65               383
  STAGE II               15                88
  STAGE III              66               124
  STAGE IV               42                58
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9P LOSS MUTATED    69  22  91   8
  9P LOSS WILD-TYPE 393 101 160   7
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              69               393
  T2              22               101
  T3              91               160
  T4               8                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9P LOSS MUTATED    71  18   2
  9P LOSS WILD-TYPE 246  25   4
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              71               246
  N1              18                25
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   125  37
  9P LOSS WILD-TYPE 417  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    125   37
  9P LOSS WILD-TYPE  417   52
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             125               417
  1              37                52
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    56 135
  9P LOSS WILD-TYPE 231 437
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     56  135
  9P LOSS WILD-TYPE  231  437
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              56               231
  MALE               135               437
[1] 2 2
[1] FALSE
D58V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9P LOSS MUTATED                   10                               149
  9P LOSS WILD-TYPE                 56                               375
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9P LOSS MUTATED                                      32
  9P LOSS WILD-TYPE                                   237
D58V9, multiclass
                                       clus
vv                                      9P LOSS MUTATED 9P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                 149               375
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              32               237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V10, continuous
D58V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     3
  9P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          14   169
  9P LOSS WILD-TYPE                       102   533
D58V12, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                     14               102
  WHITE                                        169               533
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V13, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     7 132
  9P LOSS WILD-TYPE  35 465
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7  132
  9P LOSS WILD-TYPE   35  465
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO             132               465
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   110  80
  9Q LOSS WILD-TYPE 522 131
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              190               653 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               80               131 
$`9Q LOSS MUTATED`
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8427 
      141.73        23.84        84.89        71.41        62.37         0.99 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8408 TCGA-KO-8415 TCGA-A3-3306 TCGA-A3-3311 
       42.35        10.68        16.67        57.17        36.82        39.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3346 TCGA-A3-3347 
       49.08        49.02        37.15        24.69         4.50        52.93 
TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3436 
       18.44        24.16        18.87       109.91        29.10        67.20 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3456 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
       42.08        58.49        37.58        40.70         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4815 
        3.48        19.73         3.16        43.96        46.59        52.21 
TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 
       33.50         6.02        40.44        36.53        10.09        40.70 
TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       56.68        65.29        29.03        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5113 TCGA-B0-5116 
       21.86        52.08        62.89        30.48        11.80        21.60 
TCGA-B0-5402 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 
       14.76        15.78        56.78        56.94        11.77        21.57 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 
        0.23         5.46        25.55        23.01        20.91         6.38 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4342 
        0.53        90.28        32.61        89.36        64.27        74.17 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4763 TCGA-BP-4768 
       62.86        31.89        11.31        12.33        41.75        13.15 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 
       68.38        11.64        15.78        36.39        10.98         6.71 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4985 
       71.41        58.68        60.30        61.22        45.50        31.30 
TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5009 TCGA-BP-5010 
       25.81        43.00        45.07        18.51        36.23        28.87 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 
        6.35        30.64        62.86        74.40        42.44        27.02 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4638 
       31.79        33.47        19.82        31.27        46.55        14.17 
TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4888 
       21.24        79.66        74.27        64.27        66.21        51.52 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4895 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4907 
       68.55        26.93        39.45        56.35        47.67        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5676 
       50.33        54.48        38.56         4.57        63.88        84.66 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5689 TCGA-CJ-6027 
       25.71        22.32        25.25        61.91        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 
       53.42        75.58        62.66         7.36        64.57         5.39 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       66.31        83.90        18.77        47.08        69.21         6.77 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 
       58.82        56.28        10.85        10.22        47.54        22.52 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5576 TCGA-DV-A4W0 
       31.10        67.96        65.65        14.63        23.90        66.02 
TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A84U TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       70.13        19.43        15.25        54.64        51.52        35.67 
TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ 
       12.82        18.21        19.63        12.99         9.63        49.25 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5888 
       10.09        34.49         2.10        14.86        22.92        13.25 
TCGA-BQ-5889 TCGA-BQ-7048 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DZ-6131 TCGA-F9-A4JJ 
       10.88        93.34        26.27        20.12        79.86        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC 
       13.08         4.01        11.05        34.82        13.68        17.33 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-UN-AAZ9 TCGA-Y8-A896 
        2.04         0.13        18.02        18.64 

$`9Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       109.22       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8344 
       86.56        28.11        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74       151.96        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 
       80.38        87.78       103.27        86.10        77.85        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 
       63.95        12.66        12.16        47.21         0.53        24.16 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       49.58        48.59        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       21.86        34.29        31.07        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        60.92        72.07        68.61        57.37        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       48.36        40.01        48.69        45.93        28.73        22.45 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4688 
       38.40        31.27        28.04        12.13         1.41         3.32 
TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 
       15.72         0.59         5.52        45.07        16.77        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        78.44        68.71        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
       53.88         6.71        11.64        10.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5099 
       11.90         7.30        25.32        18.51        15.09        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        29.95        19.30        35.90 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       37.22        79.17       112.80        48.89       101.13        46.68 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       60.33        84.92        90.12        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       97.41        32.61        35.90         1.68        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        10.36        32.98        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       17.16        16.60        14.27        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85         0.43        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       62.24        61.78        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4344 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       44.94        12.23        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 
       77.98        77.62         5.98        44.15        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 
       56.91        60.95        48.95        36.53        20.38        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 
       36.95        47.97         6.94        87.45        63.62        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        5.82        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        48.10        79.30         1.78        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        49.15        38.30        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95        59.84        63.25        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 
       83.97        49.25        47.18        75.06        77.36        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 
       61.91        57.83        69.86        64.18        30.64        63.98 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
       50.01        24.66        27.65        59.44        50.24        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       51.29        58.92        49.18        45.14         3.06        18.81 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       72.00        79.89        18.87        18.15        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
       67.00        83.77        92.02        81.83        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        58.75        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        61.41        63.42         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 
       18.44        55.33        56.94        55.33        47.01        21.76 
TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 
       57.21         2.40         1.94        12.69        80.19        12.26 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
       11.67        37.15        66.28        56.84        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 
        6.77         4.18         7.96        10.29        35.87         2.01 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       11.57        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       44.61         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
       20.61         0.46         1.15        15.12        43.99        22.06 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         6.81         0.16        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
       19.27         8.88        63.72        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
       40.83        26.04        30.28        26.04        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7058 
       96.92        44.84        61.28        50.40        49.84        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
       14.63         3.02        40.77        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        19.00        24.89         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 
        0.43        51.78        48.62        39.25        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25         5.49        16.80        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
       67.17        22.26        21.34        16.34        12.36        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
       12.99        26.01        29.00        18.64        15.91        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.13              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           141.73            194.79 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            31.84             29.95 
[1] "0.1 - 141.7 (31.8)" "0.1 - 194.8 (29.9)"
[1] "hr=" "2.2"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        63       19        69       40
  9Q LOSS WILD-TYPE     385       84       121       60
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                63               385
  STAGE II               19                84
  STAGE III              69               121
  STAGE IV               40                60
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  9Q LOSS MUTATED    66  23  97   6
  9Q LOSS WILD-TYPE 396 100 154   9
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              66               396
  T2              23               100
  T3              97               154
  T4               6                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  9Q LOSS MUTATED    73  17   2
  9Q LOSS WILD-TYPE 244  26   4
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              73               244
  N1              17                26
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   128  36
  9Q LOSS WILD-TYPE 414  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    128   36
  9Q LOSS WILD-TYPE  414   53
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             128               414
  1              36                53
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    56 137
  9Q LOSS WILD-TYPE 231 435
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     56  137
  9Q LOSS WILD-TYPE  231  435
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              56               231
  MALE               137               435
[1] 2 2
[1] FALSE
D59V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9Q LOSS MUTATED                   11                               150
  9Q LOSS WILD-TYPE                 55                               374
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9Q LOSS MUTATED                                      32
  9Q LOSS WILD-TYPE                                   237
D59V9, multiclass
                                       clus
vv                                      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 11                55
  KIDNEY CLEAR CELL RENAL CARCINOMA                 150               374
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              32               237
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V10, continuous
D59V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     3
  9Q LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          14   171
  9Q LOSS WILD-TYPE                       102   531
D59V12, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                12
  BLACK OR AFRICAN AMERICAN                     14               102
  WHITE                                        171               531
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V13, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9 130
  9Q LOSS WILD-TYPE  33 467
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9  130
  9Q LOSS WILD-TYPE   33  467
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                33
  NOT HISPANIC OR LATINO             130               467
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    92  36
  10P LOSS WILD-TYPE 540 175
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               128                715 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                36                175 
$`10P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       71.41        54.74        62.37        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 
       52.27        87.12         2.50        59.08       115.00        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3346 
      103.27        77.85        57.17        61.58        63.95         4.50 
TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-A6NN TCGA-AK-3433 TCGA-AK-3440 
       18.44        43.20        18.64         0.10        72.07        57.37 
TCGA-AK-3443 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4696 
       46.78        38.40        28.04        12.13         3.32        28.47 
TCGA-B0-4699 TCGA-B0-4712 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4843 
        3.62        43.96        46.59         6.02        10.09        11.64 
TCGA-B0-4845 TCGA-B0-5117 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 TCGA-B8-4143 
       65.29        17.59        32.61        21.57         0.53        23.31 
TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4161 TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4334 
        6.38        14.27        90.28        32.61         0.43        21.21 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4797 
       62.86        31.89        11.31        10.82        60.59        36.39 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 
        6.71        71.41        45.50        31.30        43.00         6.35 
TCGA-BP-5173 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4874 
        1.78        33.47        19.82        31.27        46.55        75.06 
TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4923 
       61.91        24.66        59.44        47.67        49.28        18.81 
TCGA-CJ-5676 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 
       84.66        83.90         6.77        55.33        47.01        47.54 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-DV-5566 TCGA-EU-5907 TCGA-G6-A8L8 
       31.10        12.69        80.19        45.96         4.18        35.87 
TCGA-2Z-A9J8 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B9-4116 TCGA-B9-A44B 
       67.30        12.99         9.63        49.25        20.61         2.10 
TCGA-BQ-5876 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
       19.27        79.86         4.01        13.68        25.84        17.33 
TCGA-GL-7966 TCGA-Q2-A5QZ 
        3.68        14.07 

$`10P LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      141.73       109.22        28.80       151.96        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.06        31.33        23.47        25.91         3.55         0.99 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
       19.33        11.21        42.35       100.87        87.78        86.10 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 
       12.66        12.16        36.82        47.21         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       24.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       34.29        31.07        52.93        45.53        29.92        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 
       74.76        24.16        53.29        55.76        20.71        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       22.45        37.58        31.27        40.70         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 
        4.57         2.53         3.48        19.00         1.38        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4713 
        7.82         5.98         2.14        19.73         3.16         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        20.25        15.72         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4846 
       27.42        53.88         6.71        56.68        10.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        61.32        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       21.30        31.30        11.77        10.36        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 
        9.57         5.75         0.23         1.25         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       16.60         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 
       16.27        14.17       111.02        85.51        94.72       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       93.34        99.85        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        80.68        37.25        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 
       93.99        18.48        52.24        74.17        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        61.68         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        87.45        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       48.89        49.38         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5174 
       35.21        36.23        28.87        48.10        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95        59.84        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 
       74.27        77.36        64.27        71.87        66.21        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       26.93        50.01        27.65        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 
       38.56        45.14         3.06         4.57        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       79.89        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 
       78.18        74.66         1.35       105.93       103.43        18.77 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        10.85        10.22        21.76        57.21 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       22.52         2.40         1.94        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
       18.12         3.91         6.77         7.96        10.29        70.13 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       30.35        25.08        44.61         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       10.16        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       15.12        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
       14.86        17.49        12.30        86.76         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        48.62        11.05        39.25        34.82        25.15 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.10               0.07 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            137.06             194.79 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              44.4               29.0 
[1] "0.1 - 137.1 (44.4)" "0.1 - 194.8 (29.0)"
[1] "hr=" "1.1"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        42       26        41       19
  10P LOSS WILD-TYPE     406       77       149       81
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 42                406
  STAGE II                26                 77
  STAGE III               41                149
  STAGE IV                19                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10P LOSS MUTATED    43  28  53   5
  10P LOSS WILD-TYPE 419  95 198  10
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               43                419
  T2               28                 95
  T3               53                198
  T4                5                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10P LOSS MUTATED    64   6   3
  10P LOSS WILD-TYPE 253  37   3
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               64                253
  N1                6                 37
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V6, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    83  14
  10P LOSS WILD-TYPE 459  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     83   14
  10P LOSS WILD-TYPE  459   75
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               83                459
  1               14                 75
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    46  83
  10P LOSS WILD-TYPE 241 489
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     46   83
  10P LOSS WILD-TYPE  241  489
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               46                241
  MALE                 83                489
[1] 2 2
[1] FALSE
D60V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10P LOSS MUTATED                   48                                67
  10P LOSS WILD-TYPE                 18                               457
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10P LOSS MUTATED                                      14
  10P LOSS WILD-TYPE                                   255
D60V9, multiclass
                                       clus
vv                                      10P LOSS MUTATED 10P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  48                 18
  KIDNEY CLEAR CELL RENAL CARCINOMA                   67                457
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               14                255
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V10, continuous
D60V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     2
  10P LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          12   111
  10P LOSS WILD-TYPE                       104   591
D60V12, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                      12                104
  WHITE                                         111                591
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V13, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     8  72
  10P LOSS WILD-TYPE  34 525
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8   72
  10P LOSS WILD-TYPE   34  525
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 34
  NOT HISPANIC OR LATINO               72                525
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   108  44
  10Q LOSS WILD-TYPE 524 167
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               152                691 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                44                167 
$`10Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       71.41        54.74        62.37        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       52.27        87.12         2.50        59.08       115.00        42.35 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       80.38       103.27        77.85        57.17        61.58        63.95 
TCGA-A3-3316 TCGA-A3-3331 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 
       49.08        48.82         4.50        18.44        43.20        18.64 
TCGA-A3-A6NN TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 TCGA-AK-3461 
        0.10        72.07        57.37        46.78        38.40        28.04 
TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4712 
       12.13         3.32         1.41        28.47         3.62        43.96 
TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4837 
       20.25        46.59         6.02        10.09        40.70        45.30 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5099 TCGA-B0-5117 TCGA-B0-5402 
       11.64        10.29        65.29        15.95        17.59        14.76 
TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 TCGA-B4-5838 
       39.55        79.36        32.61        21.57         0.53         5.46 
TCGA-B8-4143 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4164 
       23.31         6.38        14.27        16.27        90.28        32.61 
TCGA-BP-4166 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4351 
        0.43        27.78        21.21        74.17        62.86        31.89 
TCGA-BP-4766 TCGA-BP-4770 TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 
       48.07        10.82        60.59        36.39         6.71        71.41 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5180 
       45.50        31.30        43.00         6.35         1.78        74.40 
TCGA-BP-5185 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 
       37.22        33.47        19.82        31.27        46.55        53.52 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 
       47.18        75.06        61.91        24.66        59.44        47.67 
TCGA-CJ-4907 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-6090 
       49.28        18.81        84.66        83.77         7.36        83.90 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 
        6.77        55.33        47.01        47.54        31.10        12.69 
TCGA-CZ-5982 TCGA-DV-5565 TCGA-DV-5566 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-2Z-A9J8 
       80.19        43.69        45.96         4.18        35.87        67.30 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5876 TCGA-DZ-6131 
       12.99         9.63        49.25         2.10        19.27        79.86 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 
        4.01        13.68        25.84        17.33         3.68         0.13 
TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       14.07        86.27 

$`10Q LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 
      141.73       109.22        28.80       151.96        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 
       51.06        31.33        23.47        25.91         3.55         0.99 
TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z 
       19.33        11.21       100.87        87.78        86.10        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
       24.69        37.38        21.86        34.29        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       45.53        29.92        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       15.39        22.65         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       68.61        67.20        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       48.69        45.93        28.73        22.45        37.58        31.27 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       40.70         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        1.38        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        3.16         6.64         3.25        15.72         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
       52.21        45.07        33.50        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 
       14.93        54.48        29.10        78.44        68.71        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       53.88         6.71        56.68        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        52.08        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       56.94        52.77       120.59       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        61.32        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       21.30        31.30        11.77        10.36        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
        9.57         5.75         0.23         1.25         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
        0.23        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A8YJ 
        1.74         8.42         4.93        17.36        15.42        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
      111.02        85.51        94.72       101.06        93.34        99.85 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4330 TCGA-BP-4331 
       54.90        97.45        53.42         3.58        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        20.38        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       37.25        36.95        47.97         6.94        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 
       58.98        14.24        48.89        49.38         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
       79.30        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       49.15        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4637 
       44.55        34.95         0.95        59.84        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 
       21.24        83.97        49.25        79.66        74.27        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        66.21        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       27.65        39.45        50.24        56.35        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       58.92        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        3.06         4.57        63.88        72.00        79.89        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
       62.66        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        56.28        56.94        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5984 
       21.76        57.21        22.52         2.40         1.94        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5567 
       65.65        12.26        14.63        22.78        62.63        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.02        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       70.13         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
        4.57        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
        0.46         1.15        15.12        43.99        22.06        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
       40.83        26.04        30.28        26.04        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       10.88         7.66         0.95        11.97         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
      123.62        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       34.82        25.15         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       21.93         0.53        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.10               0.07 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            137.06             194.79 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            43.825             28.800 
[1] "0.1 - 137.1 (43.8)" "0.1 - 194.8 (28.8)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        51       32        48       23
  10Q LOSS WILD-TYPE     397       71       142       77
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 51                397
  STAGE II                32                 71
  STAGE III               48                142
  STAGE IV                23                 77
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q LOSS MUTATED    52  34  61   7
  10Q LOSS WILD-TYPE 410  89 190   8
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               52                410
  T2               34                 89
  T3               61                190
  T4                7                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  10Q LOSS MUTATED    72   9   3
  10Q LOSS WILD-TYPE 245  34   3
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               72                245
  N1                9                 34
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V6, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED   103  17
  10Q LOSS WILD-TYPE 439  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    103   17
  10Q LOSS WILD-TYPE  439   72
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              103                439
  1               17                 72
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    52 102
  10Q LOSS WILD-TYPE 235 470
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     52  102
  10Q LOSS WILD-TYPE  235  470
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               52                235
  MALE                102                470
[1] 2 2
[1] FALSE
D61V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10Q LOSS MUTATED                   49                                89
  10Q LOSS WILD-TYPE                 17                               435
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10Q LOSS MUTATED                                      16
  10Q LOSS WILD-TYPE                                   253
D61V9, multiclass
                                       clus
vv                                      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  49                 17
  KIDNEY CLEAR CELL RENAL CARCINOMA                   89                435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               16                253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V10, continuous
D61V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          13   133
  10Q LOSS WILD-TYPE                       103   569
D61V12, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 12
  BLACK OR AFRICAN AMERICAN                      13                103
  WHITE                                         133                569
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V13, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     9  89
  10Q LOSS WILD-TYPE  33 508
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9   89
  10Q LOSS WILD-TYPE   33  508
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 33
  NOT HISPANIC OR LATINO               89                508
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    26  14
  11P LOSS WILD-TYPE 606 197
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                40                803 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                14                197 
$`11P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 
      102.81        98.96        54.74        49.97         0.99        59.08 
TCGA-KN-8436 TCGA-A3-3316 TCGA-AK-3465 TCGA-B0-4696 TCGA-B0-4707 TCGA-B0-4819 
       42.35        49.08        12.13        28.47        19.73         6.02 
TCGA-B0-4822 TCGA-B0-5084 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5838 TCGA-BP-4352 
       36.53         7.30        52.77        21.57         5.46        11.31 
TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5201 TCGA-CW-5588 TCGA-CZ-5465 
       13.15        31.30         1.78        31.27        66.31        47.54 
TCGA-CZ-5469 TCGA-2Z-A9JG TCGA-4A-A93X TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-4104 
       31.10        54.64        12.82        19.63         7.33        34.49 
TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 TCGA-G7-7502 
        2.10        19.27         8.88        21.63         4.01        25.84 
TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Y8-A896 TCGA-Y8-A8S1 
       16.90         2.04        18.64        13.28 

$`11P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 
       37.58        38.40        31.27        28.04        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        3.32         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77        40.44        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
       56.78        60.33        84.92        90.12        56.94        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
       21.30        31.30        11.77        10.36        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
        9.57         5.75         0.23         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        5.98        44.15        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
       10.82         5.33        61.97        60.59        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       68.38        11.64        60.95        15.78        48.95        36.53 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       20.38        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
       47.97         6.94        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       53.65        14.93        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
       43.00        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       44.55        34.95         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       85.78        73.18        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40         1.94        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        15.25        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       75.42        34.85        56.81        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
       25.08        44.61        49.25         2.20        19.56        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       33.83        10.09        30.58        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       43.99        22.06        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       17.49        12.30        86.76        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        34.82        25.15        13.68         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        17.33        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
        5.49        16.80        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       48.30        43.76        18.02        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.05        15.62        25.28         6.74         6.02 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.99               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            102.81             194.79 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             20.65              30.64 
[1] "1.0 - 102.8 (20.6)" "0.1 - 194.8 (30.6)"
[1] "hr=" "1.9"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED        11       10        12        7
  11P LOSS WILD-TYPE     437       93       178       93
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                 11                437
  STAGE II                10                 93
  STAGE III               12                178
  STAGE IV                 7                 93
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11P LOSS MUTATED    11  10  18   1
  11P LOSS WILD-TYPE 451 113 233  14
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               11                451
  T2               10                113
  T3               18                233
  T4                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"
                    vv
clus                  N0  N1  N2
  11P LOSS MUTATED    13   6   1
  11P LOSS WILD-TYPE 304  37   5
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               13                304
  N1                6                 37
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    21   5
  11P LOSS WILD-TYPE 521  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     21    5
  11P LOSS WILD-TYPE  521   84
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               21                521
  1                5                 84
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    13  28
  11P LOSS WILD-TYPE 274 544
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     13   28
  11P LOSS WILD-TYPE  274  544
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               13                274
  MALE                 28                544
[1] 2 2
[1] FALSE
D62V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11P LOSS MUTATED                    7                                18
  11P LOSS WILD-TYPE                 59                               506
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11P LOSS MUTATED                                      16
  11P LOSS WILD-TYPE                                   253
D62V9, multiclass
                                       clus
vv                                      11P LOSS MUTATED 11P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   7                 59
  KIDNEY CLEAR CELL RENAL CARCINOMA                   18                506
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               16                253
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V10, continuous
D62V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           4    34
  11P LOSS WILD-TYPE                       112   668
D62V12, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       4                112
  WHITE                                          34                668
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V13, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  28
  11P LOSS WILD-TYPE  42 569
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   28
  11P LOSS WILD-TYPE   42  569
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               28                569
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    32  18
  11Q LOSS WILD-TYPE 600 193
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                50                793 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                18                193 
$`11Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 
      102.81        98.96        54.74        49.97         0.99        59.08 
TCGA-KN-8436 TCGA-A3-3316 TCGA-A3-3346 TCGA-AK-3425 TCGA-AK-3465 TCGA-B0-4696 
       42.35        49.08         4.50       109.91        12.13        28.47 
TCGA-B0-4707 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-5084 TCGA-B0-5702 TCGA-B2-5641 
       19.73         6.02        36.53         7.30        52.77        21.57 
TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-4986 
        0.23         5.46        11.31        13.15        31.30        25.81 
TCGA-BP-5173 TCGA-BP-5201 TCGA-CW-5588 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 
        1.78        31.27        66.31        47.54         1.94        31.10 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 
       54.64        51.52        12.82         7.33         2.10        19.27 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G 
        8.88        21.63        10.88         7.66       123.62         0.43 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 
        4.01        11.05        25.84        16.90         2.04         0.13 
TCGA-UZ-A9PQ TCGA-Y8-A896 
       86.27        18.64 

$`11Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       141.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       71.41        28.80        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       28.80        47.24       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        3.55        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
       37.38        48.82        21.86        34.29        31.07        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
        0.10        11.18        10.62        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       31.27        28.04        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        4.57         2.53         3.48        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 
       65.10         7.82         5.98         2.14         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 
        5.52        52.21        45.07        33.50        16.77        40.44 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       11.80        26.20        21.60        17.59         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       84.92        90.12        56.94        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       11.77        10.36        32.98        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        61.68        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       33.47        19.82        44.55        34.95         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       54.61        53.52        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15        61.91 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
       62.10        73.35        67.00        53.26        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       81.83         5.39        85.78        73.18        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       21.76        57.21        22.52         2.40        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       67.30        75.42        34.85        56.81        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
        5.29        16.18        22.49         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
        0.16        14.86        17.49        12.30        86.76        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35        13.25         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 
        2.76        48.26        96.92        93.34        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 
       50.40        49.84        26.27        20.12        11.28         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        2.40         1.18        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        17.33        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       12.36        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       14.83        21.93         0.53        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.91        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.13               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            123.62             194.79 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             19.50              30.71 
[1] "0.1 - 123.6 (19.5)" "0.1 - 194.8 (30.7)"
[1] "hr=" "1.9"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED        12        9        19       10
  11Q LOSS WILD-TYPE     436       94       171       90
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                 12                436
  STAGE II                 9                 94
  STAGE III               19                171
  STAGE IV                10                 90
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  11Q LOSS MUTATED    12  10  27   1
  11Q LOSS WILD-TYPE 450 113 224  14
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               12                450
  T2               10                113
  T3               27                224
  T4                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"
                    vv
clus                  N0  N1  N2
  11Q LOSS MUTATED    18   9   2
  11Q LOSS WILD-TYPE 299  34   4
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               18                299
  N1                9                 34
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    28   7
  11Q LOSS WILD-TYPE 514  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     28    7
  11Q LOSS WILD-TYPE  514   82
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               28                514
  1                7                 82
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    14  37
  11Q LOSS WILD-TYPE 273 535
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14   37
  11Q LOSS WILD-TYPE  273  535
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               14                273
  MALE                 37                535
[1] 2 2
[1] FALSE
D63V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11Q LOSS MUTATED                    7                                23
  11Q LOSS WILD-TYPE                 59                               501
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11Q LOSS MUTATED                                      21
  11Q LOSS WILD-TYPE                                   248
D63V9, multiclass
                                       clus
vv                                      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   7                 59
  KIDNEY CLEAR CELL RENAL CARCINOMA                   23                501
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               21                248
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V10, continuous
D63V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    41
  11Q LOSS WILD-TYPE                       111   661
D63V12, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       5                111
  WHITE                                          41                661
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V13, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  35
  11Q LOSS WILD-TYPE  41 562
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   35
  11Q LOSS WILD-TYPE   41  562
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               35                562
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     3   3
  12P LOSS WILD-TYPE 629 208
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 6                837 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                208 
$`12P LOSS MUTATED`
TCGA-KO-8404 TCGA-KO-8408 TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 TCGA-A4-A5Y1 
       10.68        16.67         0.43        60.59        55.33        12.99 

$`12P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       92.71        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       37.15        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        32.61        99.85        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       61.97        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       60.59        63.39        93.04         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82         0.82        23.74        18.44        56.28        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.43               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             60.59             194.79 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             14.83              30.58 
[1] "0.4 - 60.6 (14.8)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "2.9"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         1        0         4        1
  12P LOSS WILD-TYPE     447      103       186       99
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  1                447
  STAGE II                 0                103
  STAGE III                4                186
  STAGE IV                 1                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P LOSS MUTATED     2   0   3   1
  12P LOSS WILD-TYPE 460 123 248  14
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                2                460
  T2                0                123
  T3                3                248
  T4                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"
                    vv
clus                  N0  N1  N2
  12P LOSS MUTATED     1   2   0
  12P LOSS WILD-TYPE 316  41   6
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                1                316
  N1                2                 41
  N2                0                  6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3   0
  12P LOSS WILD-TYPE 539  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE  539   89
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                3                539
  1                0                 89
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1   5
  12P LOSS WILD-TYPE 286 567
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1    5
  12P LOSS WILD-TYPE  286  567
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                1                286
  MALE                  5                567
[1] 2 2
[1] FALSE
D64V8, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                114 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8443 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KM-8476         TCGA-KM-8477         TCGA-KM-8639 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-3Z-A93Z 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5465 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4W0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-4A-A93X         TCGA-4A-A93Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12P LOSS MUTATED                    2                                 3
  12P LOSS WILD-TYPE                 64                               521
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12P LOSS MUTATED                                       1
  12P LOSS WILD-TYPE                                   268
D64V9, multiclass
                                       clus
vv                                      12P LOSS MUTATED 12P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                    3                521
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V10, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 90 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8433         TCGA-KO-8409 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KO-8416         TCGA-A3-A8CQ         TCGA-A3-A8OV 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-4621 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JK         TCGA-2Z-A9JM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-2Z-A9JQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-8310 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4115         TCGA-B9-4117 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A69E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7963 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DD         TCGA-HE-A5NI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IZ-A6M8         TCGA-MH-A854 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D64V11, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 1                 66 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-A3-A8OV         TCGA-A3-A8OW 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-DV-A4W0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P LOSS MUTATED                                  0     0
  12P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           0     6
  12P LOSS WILD-TYPE                       116   696
D64V12, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       0                116
  WHITE                                           6                696
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V13, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0   4
  12P LOSS WILD-TYPE  42 593
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    4
  12P LOSS WILD-TYPE   42  593
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO                4                593
[1] 2 2
[1] FALSE

Clustering(65) Variable = 12Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED     3   1
  12Q LOSS WILD-TYPE 629 210
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                839 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                210 
$`12Q LOSS MUTATED`
TCGA-KO-8404 TCGA-BP-4166 TCGA-BP-4775 TCGA-CZ-5457 
       10.68         0.43        60.59        55.33 

$`12Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
      115.00        42.35       100.87        76.90        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 
       92.71        16.67        80.38        87.78       103.27        86.10 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       77.85        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       72.07        68.61        67.20        57.37        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 
       42.08        40.01        58.49        48.69        45.93        28.73 
TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       22.45        37.58        38.40        31.27        28.04        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       40.70         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        3.48        28.47        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4167 
       90.28       101.06        93.34        32.61        99.85        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
       41.75        71.80        48.07        13.15        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 
        1.35       105.93        83.90       103.43        18.77        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       46.16         0.59        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       57.21        47.54        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       22.78        62.63        43.69        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       54.64        51.52        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 
       22.49         0.13        12.82        11.57        18.21        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       16.96         8.48        16.31        15.75         8.28        12.99 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       48.62        11.05        39.25        34.82        25.15        13.68 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84         6.38        17.98        17.33        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       16.34        12.36         0.13        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
       50.60        78.90        12.85        17.75        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       18.02        60.03        14.83        21.93         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.43               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             60.59             194.79 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            33.005             30.480 
[1] "0.4 - 60.6 (33.0)"  "0.1 - 194.8 (30.5)"
[1] "hr=" "1.2"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         1        0         2        1
  12Q LOSS WILD-TYPE     447      103       188       99
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                447
  STAGE II                 0                103
  STAGE III                2                188
  STAGE IV                 1                 99
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12Q LOSS MUTATED     1   0   2   1
  12Q LOSS WILD-TYPE 461 123 249  14
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                461
  T2                0                123
  T3                2                249
  T4                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"
                    vv
clus                  N0  N1  N2
  12Q LOSS MUTATED     1   0   0
  12Q LOSS WILD-TYPE 316  43   6
D65V5, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                365 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8328 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8329         TCGA-KL-8330         TCGA-KL-8331 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8332         TCGA-KL-8333         TCGA-KL-8334 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8336         TCGA-KL-8337 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8338         TCGA-KL-8339         TCGA-KL-8340 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8342         TCGA-KL-8343 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8344         TCGA-KL-8345         TCGA-KL-8346 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8443         TCGA-KN-8418 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8419         TCGA-KN-8421         TCGA-KN-8422 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8423         TCGA-KN-8424         TCGA-KN-8425 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8427         TCGA-KN-8428         TCGA-KN-8429 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8430         TCGA-KO-8405         TCGA-KO-8406 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KO-8407         TCGA-KO-8408         TCGA-KO-8409 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KO-8410         TCGA-KO-8413         TCGA-KO-8414 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KO-8415         TCGA-KO-8416         TCGA-KO-8417 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-3Z-A93Z         TCGA-A3-3306         TCGA-A3-3307 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3308         TCGA-A3-3313         TCGA-A3-3317 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3331         TCGA-A3-3335         TCGA-A3-3343 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3347         TCGA-A3-3349         TCGA-A3-3351 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3352         TCGA-A3-3357         TCGA-A3-3358 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3359         TCGA-A3-3362         TCGA-A3-3363 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3367         TCGA-A3-3370         TCGA-A3-3373 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3374         TCGA-A3-3376         TCGA-A3-3378 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3380         TCGA-A3-3385         TCGA-A3-3387 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3425         TCGA-AK-3426         TCGA-AK-3427 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3428         TCGA-AK-3429         TCGA-AK-3430 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3433         TCGA-AK-3436         TCGA-AK-3443 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3450         TCGA-AK-3451         TCGA-AK-3456 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4688         TCGA-B0-4690         TCGA-B0-4691 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4693         TCGA-B0-4696         TCGA-B0-4699 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4701         TCGA-B0-4703         TCGA-B0-4710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4810         TCGA-B0-4811         TCGA-B0-4814 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4816         TCGA-B0-4817         TCGA-B0-4821 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4823         TCGA-B0-4824         TCGA-B0-4827 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4833         TCGA-B0-4834         TCGA-B0-4837 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B0-4839         TCGA-B0-4842 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4843         TCGA-B0-4846         TCGA-B0-4852 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-4945         TCGA-B0-5075         TCGA-B0-5077 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5080         TCGA-B0-5081         TCGA-B0-5084 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5085         TCGA-B0-5088         TCGA-B0-5092 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5094         TCGA-B0-5095         TCGA-B0-5096 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5097         TCGA-B0-5104         TCGA-B0-5106 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5107         TCGA-B0-5108         TCGA-B0-5109 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5110         TCGA-B0-5113         TCGA-B0-5115 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5116         TCGA-B0-5119         TCGA-B0-5120 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5121         TCGA-B0-5399         TCGA-B0-5400 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5691         TCGA-B0-5692         TCGA-B0-5694 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5696         TCGA-B0-5697 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5698         TCGA-B0-5699         TCGA-B0-5701 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5702         TCGA-B0-5703         TCGA-B0-5705 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5706         TCGA-B0-5710         TCGA-B0-5712 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5713         TCGA-B2-5633         TCGA-B2-5641 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4148         TCGA-B8-4151 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-4154         TCGA-B8-4619         TCGA-B8-4620 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-4621         TCGA-B8-4622         TCGA-B8-5158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-5159         TCGA-B8-5163         TCGA-B8-5164 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-5165         TCGA-B8-5545         TCGA-B8-5546 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-5549         TCGA-B8-5550         TCGA-B8-5551 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-5553         TCGA-B8-A54H         TCGA-BP-4158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4159         TCGA-BP-4160         TCGA-BP-4162 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4163         TCGA-BP-4165         TCGA-BP-4169 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4170         TCGA-BP-4173         TCGA-BP-4174 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4325         TCGA-BP-4326         TCGA-BP-4327 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4329         TCGA-BP-4330         TCGA-BP-4331 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4332         TCGA-BP-4334         TCGA-BP-4335 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4337         TCGA-BP-4338         TCGA-BP-4340 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4342         TCGA-BP-4343         TCGA-BP-4346 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4351         TCGA-BP-4352         TCGA-BP-4353 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4354         TCGA-BP-4756         TCGA-BP-4761 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4768         TCGA-BP-4770         TCGA-BP-4771 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4787         TCGA-BP-4795         TCGA-BP-4797 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4798         TCGA-BP-4799         TCGA-BP-4960 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4964         TCGA-BP-4967         TCGA-BP-4968 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4970         TCGA-BP-4971         TCGA-BP-4974 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4985         TCGA-BP-4986         TCGA-BP-4988 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4989         TCGA-BP-4995         TCGA-BP-5006 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5007         TCGA-BP-5010         TCGA-BP-5169 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5182         TCGA-BP-5186         TCGA-BP-5191 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5198         TCGA-BP-5199         TCGA-BP-5201 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4636         TCGA-CJ-4638         TCGA-CJ-4639 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4640         TCGA-CJ-4643         TCGA-CJ-4644 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4868         TCGA-CJ-4869         TCGA-CJ-4872 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4873         TCGA-CJ-4874         TCGA-CJ-4876 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4890         TCGA-CJ-4891         TCGA-CJ-4892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4894         TCGA-CJ-4900         TCGA-CJ-4904 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4918         TCGA-CJ-5678         TCGA-CJ-6030 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-6033         TCGA-CW-5584         TCGA-CW-5585 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CW-5587         TCGA-CW-5591         TCGA-CW-6087 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CW-6088         TCGA-CZ-4854         TCGA-CZ-4856 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4857         TCGA-CZ-4859         TCGA-CZ-4863 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4864         TCGA-CZ-5451         TCGA-CZ-5452 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5454         TCGA-CZ-5456         TCGA-CZ-5467 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5470         TCGA-CZ-5984 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5985         TCGA-CZ-5986         TCGA-CZ-5988 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5989         TCGA-G6-A5PC         TCGA-G6-A8L7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J1         TCGA-2Z-A9JO         TCGA-4A-A93W 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-7583         TCGA-A4-7585         TCGA-A4-7915 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y1         TCGA-A4-A7UZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-3473 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-5398         TCGA-B1-A47O 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B1-A655         TCGA-B1-A656         TCGA-B1-A657 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-BQ-5877         TCGA-BQ-5878 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-5879         TCGA-BQ-5880         TCGA-BQ-5882 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-5885         TCGA-BQ-5887         TCGA-BQ-5888 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-5889         TCGA-BQ-5890         TCGA-BQ-5891 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-5892         TCGA-BQ-5893         TCGA-BQ-5894 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-7045         TCGA-BQ-7048         TCGA-BQ-7050 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-7051         TCGA-BQ-7056         TCGA-BQ-7058 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-DZ-6131         TCGA-F9-A8NY 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6789         TCGA-G7-6793 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LD 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GL-6846         TCGA-GL-7966         TCGA-GL-A59R 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-GL-A9DC         TCGA-IA-A40U         TCGA-IA-A40Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IA-A83W         TCGA-J7-6720         TCGA-J7-8537 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KV-A74V         TCGA-P4-A5E6         TCGA-P4-A5E8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-P4-A5EA         TCGA-SX-A71R         TCGA-SX-A7SM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SS         TCGA-UN-AAZ9 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PQ         TCGA-UZ-A9PX 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-Y8-A897         TCGA-Y8-A8RZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   0
  12Q LOSS WILD-TYPE 539  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE  539   89
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                3                539
  1                0                 89
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1   3
  12Q LOSS WILD-TYPE 286 569
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    3
  12Q LOSS WILD-TYPE  286  569
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                286
  MALE                  3                569
[1] 2 2
[1] FALSE
D65V8, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                114 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8443 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KM-8476         TCGA-KM-8477         TCGA-KM-8639 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-3Z-A93Z 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5465 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5469         TCGA-CZ-5982         TCGA-DV-5565 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4W0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-4A-A93X         TCGA-4A-A93Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6793         TCGA-G7-6796 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A7SO         TCGA-SX-A7SP         TCGA-SX-A7SQ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-SX-A7SU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12Q LOSS MUTATED                    1                                 3
  12Q LOSS WILD-TYPE                 65                               521
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                   269
D65V9, multiclass
                                       clus
vv                                      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   1                 65
  KIDNEY CLEAR CELL RENAL CARCINOMA                    3                521
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                0                269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V10, continuous
D65V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           0     4
  12Q LOSS WILD-TYPE                       116   698
D65V12, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       0                116
  WHITE                                           4                698
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V13, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0   2
  12Q LOSS WILD-TYPE  42 595
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE   42  595
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO                2                595
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    86  48
  13Q LOSS WILD-TYPE 546 163
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               134                709 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                48                163 
$`13Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 
       38.07       141.73       137.06       102.81        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       98.96        84.89        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 
       86.56        28.11        66.54        24.79       151.96        44.91 
TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       47.24       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00        76.90        10.68        74.93        79.04 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67        80.38        77.85        61.58        63.95 
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3426 
       37.15         4.50        52.93        74.76        43.20        29.10 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
       72.07        57.37        42.08        12.13        40.70         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 
        1.41         4.57        28.47         1.38         3.62        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       43.96        52.21         6.02        15.09        10.95         8.05 
TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5696 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       11.80        17.59        56.78         0.23         0.53         5.46 
TCGA-B8-5163 TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4343 
       27.02         6.38        89.36        21.21        93.99        62.86 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4964 
       11.31        33.99        13.15        10.82        15.78        61.22 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5175 
       57.40        45.50        31.30        43.00        37.02        30.64 
TCGA-BP-5191 TCGA-CJ-4868 TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CJ-5677 TCGA-CJ-5679 
       31.79        21.24        66.21        47.67        25.71        22.32 
TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4860 
       53.42        66.31        83.90        18.77        46.16         6.77 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 
       63.39        61.41        18.44        55.33        47.54         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 TCGA-G6-A8L7 TCGA-2Z-A9JI TCGA-A4-7287 
       31.10        67.96        12.16        70.13        51.52        19.63 
TCGA-A4-7915 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B3-A6W5 TCGA-BQ-5875 TCGA-BQ-5879 
        0.23        49.25        10.09        10.16        86.76        22.92 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 
        2.76        10.68        13.08         4.01        11.05        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 
       17.33        16.90         3.68         2.04         0.13        42.94 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       14.07        18.02 

$`13Q LOSS WILD-TYPE`
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       23.84       109.22        98.33        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 
       54.74        62.37        23.28        28.80        49.97        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 
       31.33        23.47        25.91         3.55        11.21        42.35 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 TCGA-3Z-A93Z 
      100.87        87.78       103.27        86.10        57.17        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.16        36.82        47.21         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        49.02        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
       10.62       109.91        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
       60.92        68.61        67.20        46.78        48.36        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4694 
       38.40        31.27        28.04         1.41         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
       19.00        65.10         7.82         5.98         2.14         3.16 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 
        5.52        45.07        33.50        16.77        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5096 TCGA-B0-5097 
       11.90         7.30        25.32        18.51         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 
       30.48        29.95        19.30        35.90        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
       16.67         9.57         5.75         1.25         4.64         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74         1.18         0.85        24.23        17.16        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       14.27         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
      101.06        93.34        32.61        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 
       15.16         0.07        18.48        52.24        74.17        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        12.33        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       48.95        36.53        20.38        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
       63.62        58.68        60.30        61.51         6.74        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       14.24        48.89        49.38         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        18.51        38.70        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        1.78        74.20        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 
       65.69        54.61        53.52        58.95        11.05        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
       63.88        72.00        79.89        84.66        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       60.99        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 
       92.02        81.83         5.39        85.78        73.18        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
       74.66         1.35       105.93       103.43        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4864 
       47.08        69.21        58.75        14.66        60.59        93.04 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5456 
        5.46        63.42        58.82         0.82        23.74        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       57.21        22.52         2.40        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       65.88        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       66.02        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       54.64        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 
        0.13        12.82        11.57        18.21        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       35.18        19.13         0.89        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       76.64        13.55        30.35        25.08        44.61         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
       19.56         7.33        21.67        24.56        16.87         3.55 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       16.77         0.46         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
        6.81         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95        11.97         7.92       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       19.00        24.89         2.40         1.18         0.43        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       48.62        39.25        34.82        25.15        13.68         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       25.97        21.44        15.48        99.78        87.22         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       26.47        48.30        43.76        60.03        14.83        21.93 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.13               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            151.96             194.79 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            37.085             29.920 
[1] "0.1 - 152.0 (37.1)" "0.1 - 194.8 (29.9)"
[1] "hr=" "1.4"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        43       21        45       27
  13Q LOSS WILD-TYPE     405       82       145       73
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 43                405
  STAGE II                21                 82
  STAGE III               45                145
  STAGE IV                27                 73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED    45  23  59   9
  13Q LOSS WILD-TYPE 417 100 192   6
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               45                417
  T2               23                100
  T3               59                192
  T4                9                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  13Q LOSS MUTATED    63  14   4
  13Q LOSS WILD-TYPE 254  29   2
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               63                254
  N1               14                 29
  N2                4                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V6, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    80  19
  13Q LOSS WILD-TYPE 462  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     80   19
  13Q LOSS WILD-TYPE  462   70
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               80                462
  1               19                 70
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    57  79
  13Q LOSS WILD-TYPE 230 493
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     57   79
  13Q LOSS WILD-TYPE  230  493
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               57                230
  MALE                 79                493
[1] 2 2
[1] FALSE
D66V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  13Q LOSS MUTATED                   43                                71
  13Q LOSS WILD-TYPE                 23                               453
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  13Q LOSS MUTATED                                      22
  13Q LOSS WILD-TYPE                                   247
D66V9, multiclass
                                       clus
vv                                      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  43                 23
  KIDNEY CLEAR CELL RENAL CARCINOMA                   71                453
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               22                247
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V10, continuous
D66V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     4
  13Q LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          12   116
  13Q LOSS WILD-TYPE                       104   586
D66V12, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                 11
  BLACK OR AFRICAN AMERICAN                      12                104
  WHITE                                         116                586
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V13, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  86
  13Q LOSS WILD-TYPE  38 511
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   86
  13Q LOSS WILD-TYPE   38  511
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               86                511
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   161  98
  14Q LOSS WILD-TYPE 471 113
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               259                584 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                98                113 
$`14Q LOSS MUTATED`
TCGA-KL-8344 TCGA-KN-8427 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       28.80         0.99        36.82        39.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3324 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3346 
       37.15        49.58        38.99        21.86        34.29         4.50 
TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 
       52.93        29.92        88.37        20.71        18.87        20.28 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3450 
       29.10        84.36        66.31        15.78        67.20        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-B0-4691 TCGA-B0-4694 
       48.69        28.73        22.45        38.40         4.57         3.48 
TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4814 TCGA-B0-4815 
        5.98        19.73        43.96         6.64         5.52        52.21 
TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 
       33.50         6.02        10.09        78.44        40.70        27.42 
TCGA-B0-4839 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       53.88        26.07        29.03        36.85        70.52        20.94 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
       11.90         7.30        15.09        10.95         2.24        21.86 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5694 
       52.54        30.48        11.80        37.22        48.89        15.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
       60.33        84.92        56.94        47.97        96.36        89.49 
TCGA-B2-4098 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
        1.68        31.30        11.77        10.36        32.98        21.57 
TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4143 TCGA-B8-4619 
        0.23         4.64         5.46         0.36        23.31        17.19 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5553 
       20.91         1.18         0.85        14.27         0.53        14.30 
TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4167 
       27.29         1.74         4.93        93.34        32.61        89.36 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4331 TCGA-BP-4343 TCGA-BP-4346 
       62.24        61.78        64.27        80.68        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 
       44.94        11.31        12.33        33.99         5.98        41.75 
TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 
       13.15         5.33        56.91        68.38        15.78        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4965 TCGA-BP-4970 
       10.98         6.71        87.45        58.68        61.51        14.24 
TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4986 
       48.89        45.50        14.93        36.07        46.45        25.81 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5009 TCGA-BP-5169 
        3.88        16.47        18.51        37.02        36.23         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5180 
       79.30         1.78        74.20        30.64        62.86        74.40 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5196 
       42.44        37.22        27.02        33.24        31.79        33.47 
TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 
       19.82        31.27        63.25        73.22        14.17        65.69 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 
       54.61        53.52        11.05        21.24        83.97        79.66 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 
       74.27        75.06        77.36        64.27        66.21        57.83 
TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 
       51.52        26.93        24.66        27.65        59.44        51.29 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 
       49.28        50.33        54.48        38.56        45.14         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-5689 
       18.87        22.32        25.25        61.91        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5587 
       60.99        75.58         7.36        64.57         5.39        73.18 
TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4854 TCGA-CZ-4858 
       66.31         1.35        83.90        18.77        46.16        69.21 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5452 
        6.77        14.66        63.39        93.04        61.41        58.82 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       18.44        56.28        10.85        10.22        21.76        47.54 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
        1.94        31.10        12.69        67.96        65.65        14.63 
TCGA-CZ-5989 TCGA-DV-5573 TCGA-G6-A5PC TCGA-MM-A563 TCGA-MM-A84U TCGA-2Z-A9JG 
       62.63        37.15         7.96        19.43        15.25        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-8098 
       51.52        38.99        18.21        19.63         0.10        29.46 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 
       12.99         9.63        25.08        44.61        49.25         7.33 
TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 
       16.77        10.09        20.61         6.81        19.27        30.28 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ 
       13.25        10.88         2.76        79.86        80.88        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       13.08         4.01        11.05        34.82        13.68        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y 
       17.33        16.90        27.65        73.25        16.80         2.04 
TCGA-MH-A854 TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PN 
        0.36         6.61        12.85        14.07        18.02        21.93 
TCGA-WN-A9G9 
       26.01 

$`14Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       24.79        73.91        71.41        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
       57.17        61.58        63.95        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3325 TCGA-A3-3326 
        0.53        24.16        48.59        36.36        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 
       48.82        31.07        45.53        18.44        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
       53.29        43.20        55.76        18.64        28.31        65.52 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
      109.91        73.08        60.92        72.07        68.61        57.37 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 
       46.78        48.36        42.08        40.01        45.93        37.58 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
        1.41         2.53        28.47        19.00         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
       65.10         7.82         2.14         3.16         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4821 
       15.72        46.59         0.59        45.07        16.77        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 
       36.53        14.93        54.48        29.10        68.71        45.30 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4849 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 
        2.27        43.30        11.24        25.32        18.51         8.05 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 
       52.08        15.95        62.89        90.87        90.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       19.30        35.90        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       16.21        18.21        21.44        14.76        79.17       112.80 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 
      101.13        46.68        56.78        90.12        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
      120.59        79.36       102.48        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       35.90        12.30        21.30        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        1.25         0.53         0.23        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 
       25.05        24.66        25.55        25.91        23.01        23.74 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 
       27.02        24.23        17.16        16.60         6.38        34.39 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
       29.88        17.06         8.42        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4177 TCGA-BP-4325 
       99.85         0.43        23.05        77.03        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       53.42         3.58        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       54.77        12.23        31.89        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98        77.62        44.15        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 
       10.82        61.97        60.59        13.51        11.64        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 
       48.95        36.53        20.38        37.25        36.95        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
        6.94        71.41        63.62        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       57.40        58.98        49.38         7.23        47.11        53.65 
TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4991 TCGA-BP-4993 
       33.34        31.30        36.95        27.22        46.45         5.82 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 
       43.00        45.07        30.64        41.62        38.70        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5176 TCGA-BP-5177 
       37.48        35.21        28.87        48.10        52.27         9.63 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 
       49.15        38.30        37.25        22.78        13.35        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       13.41        24.62        44.55        34.95         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4878 
       46.55        75.88        58.95        49.25        47.18        71.87 
TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 
       61.91        69.86        64.18        30.64        63.98        68.55 
TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       50.01        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4918 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       58.92        49.18         3.06        18.15        62.10        73.35 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       53.42        62.66        83.77        92.02        81.83        85.78 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
       78.18        74.66       105.93       103.43        25.45         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 
       47.08        58.75        60.59         5.46        63.42         0.82 
TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 
       23.74        55.33        56.94        55.33        47.01        57.21 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 
       22.52         2.40        80.19        12.26        22.78        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       45.96        65.88        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        70.13        35.87         2.01        19.96        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ 
        4.57        67.30        75.42        34.85        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       61.05        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       30.48        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       13.55        30.35         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
       16.87         3.55         0.46         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       19.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        26.04        25.35         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6133 TCGA-DZ-6134 
        3.75        14.63         3.02        40.77        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        19.00        24.89         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM 
        0.43        51.78        48.62        39.25        25.15         6.38 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
       17.98        80.65       194.79        12.92         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       13.41        11.84        56.75         5.49        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       30.38        27.65        20.25        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.22        42.94        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        25.68        27.39        12.99        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             96.36             194.79 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            29.460             30.655 
[1] "0.1 - 96.4 (29.5)"  "0.1 - 194.8 (30.7)"
[1] "hr=" "2.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        97       29        79       52
  14Q LOSS WILD-TYPE     351       74       111       48
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 97                351
  STAGE II                29                 74
  STAGE III               79                111
  STAGE IV                52                 48
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q LOSS MUTATED   104  38 114   4
  14Q LOSS WILD-TYPE 358  85 137  11
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1              104                358
  T2               38                 85
  T3              114                137
  T4                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"
                    vv
clus                  N0  N1  N2
  14Q LOSS MUTATED   101  23   3
  14Q LOSS WILD-TYPE 216  20   3
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              101                216
  N1               23                 20
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   175  49
  14Q LOSS WILD-TYPE 367  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    175   49
  14Q LOSS WILD-TYPE  367   40
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              175                367
  1               49                 40
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    84 176
  14Q LOSS WILD-TYPE 203 396
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     84  176
  14Q LOSS WILD-TYPE  203  396
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               84                203
  MALE                176                396
[1] 2 2
[1] FALSE
D67V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  14Q LOSS MUTATED                    2                               214
  14Q LOSS WILD-TYPE                 64                               310
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  14Q LOSS MUTATED                                      44
  14Q LOSS WILD-TYPE                                   225
D67V9, multiclass
                                       clus
vv                                      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  214                310
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               44                225
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V10, continuous
D67V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     3
  14Q LOSS WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          22   228
  14Q LOSS WILD-TYPE                        94   474
D67V12, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 12
  BLACK OR AFRICAN AMERICAN                      22                 94
  WHITE                                         228                474
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V13, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    13 182
  14Q LOSS WILD-TYPE  29 415
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     13  182
  14Q LOSS WILD-TYPE   29  415
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 29
  NOT HISPANIC OR LATINO              182                415
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    40  26
  15Q LOSS WILD-TYPE 592 185
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                66                777 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                26                185 
$`15Q LOSS MUTATED`
TCGA-KN-8421 TCGA-KN-8427 TCGA-A3-3319 TCGA-A3-3382 TCGA-B0-4690 TCGA-B0-4698 
       87.91         0.99        37.15        18.87         1.41         1.38 
TCGA-B0-4712 TCGA-B0-4821 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5116 
       43.96        40.44        11.24         7.30         8.05        21.60 
TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-5549 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4343 
        0.23        25.55         6.38        32.61        89.36        62.86 
TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4985 TCGA-BP-5169 
       11.31        13.15        60.59        36.39        31.30         6.35 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5200 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5677 
       30.64        62.86        34.95        47.67        49.28        25.71 
TCGA-CJ-6028 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5469 
       53.42        47.08         6.77        55.33        10.85        31.10 
TCGA-CZ-5984 TCGA-G6-A8L8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 
       67.96        35.87        54.64        51.52        12.82        18.21 
TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5879 
        0.10        12.99        19.56        10.09         6.81        22.92 
TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
       21.63        10.88         2.76        10.68        13.08         4.01 
TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 TCGA-HE-A5NK 
       34.82        25.84        17.33       194.79         3.68        73.25 
TCGA-P4-A5EA TCGA-PJ-A5Z8 TCGA-UN-AAZ9 TCGA-UZ-A9PP TCGA-Y8-A896 TCGA-Y8-A8S1 
        6.61        12.85        18.02         0.53        18.64        13.28 

$`15Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8422 
      123.12        51.06        31.33       129.37        23.47        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       57.17        61.58        63.95        12.66        12.16        36.82 
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       47.21         0.53        39.16        24.16        49.08        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4699 
        4.57         2.53         3.48        28.47        19.00         3.62 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73         3.16 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 
       11.90        25.32        18.51        15.09        10.95         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       56.94        52.77        39.55       120.59        79.36       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
       47.97        96.36        89.49        61.32        97.41        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        12.30        21.30        31.30        11.77 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       10.36        32.98        21.57        16.67         9.57         5.75 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       17.19        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        17.16        16.60        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       93.34        99.85         0.43        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 
        0.07        93.99        18.48        52.24        74.17        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        12.33        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
       31.33        12.30        72.59        77.98        77.62         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        20.38        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
       37.25        36.95         6.71        47.97         6.94        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       71.41        63.62        58.68        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
       46.45        16.47         5.82        43.00        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 
       35.21        36.23        28.87        48.10        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
       74.20        52.27         9.63        74.40        49.15        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       19.82        44.55        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       24.66        27.65        39.45        59.44        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00        79.89        84.66        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       60.99        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
       18.77        25.45        46.16         0.59        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 
       14.66        60.59        63.39        93.04         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       56.94        55.33        47.01        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       34.85        56.81        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7585 
       22.49         0.13        11.57        19.63        61.05        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 
       15.75         8.28        12.46         9.63        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        25.35        13.25         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       39.25        25.15        13.68         6.38        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       80.65        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       56.75         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       21.44        15.48        99.78        87.22        42.94        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z9 
       92.58        52.27        16.01        50.60        78.90        17.75 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       48.30        43.76        60.03        14.83        21.93        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
       26.01        29.00        18.64        15.91        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       25.28         6.74         6.02 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.10               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            194.79             151.96 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            19.215             31.200 
[1] "0.1 - 194.8 (19.2)" "0.1 - 152.0 (31.2)"
[1] "hr=" "2.3"
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q LOSS MUTATED        20        4        23       17
  15Q LOSS WILD-TYPE     428       99       167       83
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                 20                428
  STAGE II                 4                 99
  STAGE III               23                167
  STAGE IV                17                 83
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    23   4  34   5
  15Q LOSS WILD-TYPE 439 119 217  10
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               23                439
  T2                4                119
  T3               34                217
  T4                5                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  15Q LOSS MUTATED    22   9   1
  15Q LOSS WILD-TYPE 295  34   5
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               22                295
  N1                9                 34
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    34  13
  15Q LOSS WILD-TYPE 508  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34   13
  15Q LOSS WILD-TYPE  508   76
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               34                508
  1               13                 76
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    19  48
  15Q LOSS WILD-TYPE 268 524
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     19   48
  15Q LOSS WILD-TYPE  268  524
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               19                268
  MALE                 48                524
[1] 2 2
[1] FALSE
D68V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  15Q LOSS MUTATED                    2                                36
  15Q LOSS WILD-TYPE                 64                               488
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  15Q LOSS MUTATED                                      29
  15Q LOSS WILD-TYPE                                   240
D68V9, multiclass
                                       clus
vv                                      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   36                488
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               29                240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V10, continuous
D68V11, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 65 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-A3-A8OV 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-5158 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MM-A84U         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         TCGA-2Z-A9JN 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q LOSS MUTATED                                  0     2
  15Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           5    56
  15Q LOSS WILD-TYPE                       111   646
D68V12, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       5                111
  WHITE                                          56                646
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V13, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  46
  15Q LOSS WILD-TYPE  41 551
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   46
  15Q LOSS WILD-TYPE   41  551
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               46                551
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6  11
  16P LOSS WILD-TYPE 626 200
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                17                826 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                200 
$`16P LOSS MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KO-8408 TCGA-A3-3316 TCGA-A3-A6NN 
       30.25        28.11         0.99        16.67        49.08         0.10 
TCGA-B0-4696 TCGA-B0-4822 TCGA-B8-5551 TCGA-BP-4354 TCGA-BP-4770 TCGA-BP-4797 
       28.47        36.53         0.53        33.99        10.82        36.39 
TCGA-BP-4985 TCGA-CZ-5982 TCGA-A4-7287 TCGA-BQ-5882 TCGA-G7-6793 
       31.30        80.19        19.63        21.63        11.05 

$`16P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       92.55        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         3.55        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 
       76.90        10.68        74.93        79.04        92.71        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       39.16        24.16        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       20.28        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       60.92        72.07        68.61        67.20        57.37        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
       48.36        42.08        40.01        58.49        48.69        45.93 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       12.13        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53         3.48        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       40.44        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       68.71        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
        1.94        16.21        18.21        21.44        37.22        14.76 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       79.17       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       39.55       120.59        79.36       102.48        47.97        96.36 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
       89.49        61.32        97.41        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        27.16        27.55        25.05        24.66        17.19 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
       25.55        25.91        23.01        20.91        23.74         1.18 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       14.27        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        12.33        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       77.98        77.62         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        61.68         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 
       13.51        56.91        68.38        11.64        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        20.38        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       30.64        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 
       61.91        62.10        73.35        67.00        53.26        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       92.02        81.83         5.39        85.78        73.18        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       18.77        25.45        46.16         0.59        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       58.75         6.77        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40         1.94        31.10        12.69        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        15.25        10.85         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 
       58.22       100.27        56.91         4.57        67.30        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK 
       34.85        56.81        54.64        51.52        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       26.43        30.71        24.33        31.20        29.36        25.58 
TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
        5.29        16.18        22.49         0.13        12.82        11.57 
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       18.21        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.28        23.31         0.76        19.63        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       12.46        16.96         8.48        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       12.99        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
        7.33        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
        0.46         6.58        33.83        10.09        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       12.46        10.16        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        7.63         7.04         7.17         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       61.02        54.90        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       48.62        39.25        34.82        25.15        13.68        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
        6.38        17.98        17.33        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
       12.92         3.68        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25         5.49        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        84.95        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       78.90        12.85        17.75        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       60.03        14.83        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       52.11        30.67        25.68        27.39        12.99        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
       29.00        18.64        15.91        18.64        18.05        15.62 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.74         6.02        13.28 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.10               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             80.19             194.79 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             28.11              30.64 
[1] "0.1 - 80.2 (28.1)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "4"  
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         4        2         6        6
  16P LOSS WILD-TYPE     444      101       184       94
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  4                444
  STAGE II                 2                101
  STAGE III                6                184
  STAGE IV                 6                 94
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     4   2   9   3
  16P LOSS WILD-TYPE 458 121 242  12
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                4                458
  T2                2                121
  T3                9                242
  T4                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"
                    vv
clus                  N0  N1  N2
  16P LOSS MUTATED     6   4   2
  16P LOSS WILD-TYPE 311  39   4
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                6                311
  N1                4                 39
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    11   2
  16P LOSS WILD-TYPE 531  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     11    2
  16P LOSS WILD-TYPE  531   87
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               11                531
  1                2                 87
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7  11
  16P LOSS WILD-TYPE 280 561
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   11
  16P LOSS WILD-TYPE  280  561
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                280
  MALE                 11                561
[1] 2 2
[1] FALSE
D69V8, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                113 
        TCGA-KM-8438         TCGA-KM-8439         TCGA-KM-8440 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8441         TCGA-KM-8442         TCGA-KM-8443 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8476         TCGA-KM-8477         TCGA-KM-8639 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-KO-8413         TCGA-3Z-A93Z 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3430         TCGA-B0-4838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B2-5639         TCGA-B4-5377         TCGA-B4-5378 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5832         TCGA-B4-5834         TCGA-B4-5835 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5836         TCGA-B4-5838         TCGA-B4-5843 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5844         TCGA-CZ-4854         TCGA-CZ-4856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-DV-5565 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5566         TCGA-DV-5567         TCGA-DV-5568 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5573         TCGA-DV-5574 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5575         TCGA-DV-5576         TCGA-DV-A4W0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EU-5904         TCGA-EU-5905         TCGA-EU-5907 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L7         TCGA-G6-A8L8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-4A-A93X         TCGA-4A-A93Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8518 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8630         TCGA-A4-A4ZT         TCGA-A4-A57E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-5560         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7834         TCGA-DW-7836         TCGA-DW-7837 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-DW-7839         TCGA-DW-7840 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7841         TCGA-DW-7842         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5901         TCGA-EV-5902         TCGA-EV-5903 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6796         TCGA-G7-6797 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-P4-AAVK 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16P LOSS MUTATED                    4                                10
  16P LOSS WILD-TYPE                 62                               514
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16P LOSS MUTATED                                       4
  16P LOSS WILD-TYPE                                   265
D69V9, multiclass
                                       clus
vv                                      16P LOSS MUTATED 16P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                   10                514
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                4                265
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V10, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 90 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8335 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8433         TCGA-KO-8409 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8416         TCGA-A3-A8CQ         TCGA-A3-A8OV 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-4621 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JK         TCGA-2Z-A9JM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-2Z-A9JQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-8310 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4115         TCGA-B9-4117 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A69E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7963 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DD         TCGA-HE-A5NI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IZ-A6M8         TCGA-MH-A854 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D69V11, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 66 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-A3-A8OV         TCGA-A3-A8OW 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-DV-A4W0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P LOSS MUTATED                                  0     0
  16P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           2    14
  16P LOSS WILD-TYPE                       114   688
D69V12, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       2                114
  WHITE                                          14                688
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V13, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   8
  16P LOSS WILD-TYPE  42 589
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    8
  16P LOSS WILD-TYPE   42  589
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO                8                589
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11  16
  16Q LOSS WILD-TYPE 621 195
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                27                816 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                195 
$`16Q LOSS MUTATED`
TCGA-KL-8336 TCGA-KL-8339 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8408 TCGA-A3-3306 
       30.25        28.11         0.99        52.27        16.67        36.82 
TCGA-A3-3316 TCGA-A3-A6NN TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-5097 
       49.08         0.10        36.53        40.70        45.30        21.86 
TCGA-B0-5402 TCGA-B8-5551 TCGA-BP-4354 TCGA-BP-4770 TCGA-BP-4797 TCGA-BP-4985 
       14.76         0.53        33.99        10.82        36.39        31.30 
TCGA-CZ-5982 TCGA-G6-A8L8 TCGA-MM-A564 TCGA-2Z-A9JI TCGA-A4-7287 TCGA-A4-A5Y1 
       80.19        35.87        19.96        51.52        19.63        12.99 
TCGA-BQ-5882 TCGA-G7-6793 TCGA-G7-A8LD 
       21.63        11.05        16.90 

$`16Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       92.55        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 
       71.41        28.80        54.74        62.37       151.96        23.28 
TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       44.91        28.80        47.24        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       65.19       104.52         3.55        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 
       10.68        74.93        79.04        92.71        80.38        87.78 
TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.27        86.10        77.85        57.17        61.58        63.95 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        12.16        47.21         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
        4.50        52.93        45.53        29.92        18.44        88.37 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       42.97        82.32        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
       74.76        24.16        53.29        43.20        55.76        20.71 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       18.64        18.87        28.31        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
       22.65         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        31.27        28.04        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
        1.41         3.32         1.41         4.57         2.53         3.48 
TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
       28.47        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         2.14        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        20.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       21.60        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        14.27        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        12.33        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       46.45        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       47.01        10.85        10.22        21.76        57.21        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 
       22.52         2.40         1.94        31.10        12.69        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
        4.18         7.96        10.29        70.13         2.01        19.43 
TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       15.25        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       56.81        54.64        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 
       22.49         0.13        12.82        11.57        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       63.72        22.92        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        51.78        48.62        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        13.68        25.84         6.38        17.98        17.33 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        16.34        12.36         0.13        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
       16.01        50.60        78.90        12.85        17.75        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        15.62        25.28         6.74         6.02        13.28 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.10               0.07 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             80.19             194.79 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             28.11              30.61 
[1] "0.1 - 80.2 (28.1)"  "0.1 - 194.8 (30.6)"
[1] "hr=" "3.4"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         7        4         9        8
  16Q LOSS WILD-TYPE     441       99       181       92
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  7                441
  STAGE II                 4                 99
  STAGE III                9                181
  STAGE IV                 8                 92
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     8   4  12   4
  16Q LOSS WILD-TYPE 454 119 239  11
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                8                454
  T2                4                119
  T3               12                239
  T4                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"
                    vv
clus                  N0  N1  N2
  16Q LOSS MUTATED     9   6   2
  16Q LOSS WILD-TYPE 308  37   4
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                9                308
  N1                6                 37
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V6, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    14   3
  16Q LOSS WILD-TYPE 528  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     14    3
  16Q LOSS WILD-TYPE  528   86
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               14                528
  1                3                 86
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     9  19
  16Q LOSS WILD-TYPE 278 553
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   19
  16Q LOSS WILD-TYPE  278  553
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                9                278
  MALE                 19                553
[1] 2 2
[1] FALSE
D70V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16Q LOSS MUTATED                    5                                16
  16Q LOSS WILD-TYPE                 61                               508
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16Q LOSS MUTATED                                       7
  16Q LOSS WILD-TYPE                                   262
D70V9, multiclass
                                       clus
vv                                      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   5                 61
  KIDNEY CLEAR CELL RENAL CARCINOMA                   16                508
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                7                262
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V10, continuous
D70V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           4    22
  16Q LOSS WILD-TYPE                       112   680
D70V12, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       4                112
  WHITE                                          22                680
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V13, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0  18
  16Q LOSS WILD-TYPE  42 579
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0   18
  16Q LOSS WILD-TYPE   42  579
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               18                579
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    75  28
  17P LOSS WILD-TYPE 557 183
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               103                740 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                28                183 
$`17P LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       54.74        62.37       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00        42.35        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       16.67        80.38       103.27        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3382 
       63.95        49.08        37.15         4.50        43.20        18.87 
TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3456 TCGA-AK-3465 
       72.07        67.20        57.37        40.01        37.58        12.13 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4813 TCGA-B0-4817 
       40.70         3.62        19.73        43.96         0.59        33.50 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-5117 TCGA-B0-5702 TCGA-B2-3923 TCGA-B4-5835 
       78.44        40.70        17.59        52.77        32.61         0.53 
TCGA-BP-4166 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4787 
        0.43        64.27        21.21        31.89        11.31        15.78 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4994 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4871 
       36.39        10.98        43.00        33.47        19.82        79.66 
TCGA-CJ-4872 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-4860 
       47.18        84.66        25.71        66.31        69.21         6.77 
TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-DV-5565 TCGA-G6-A8L7 TCGA-2Z-A9JI 
       47.01        47.54         1.94        43.69        70.13        51.52 
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-A57E TCGA-AL-3466 TCGA-BQ-7058 TCGA-G7-6793 
       19.63         0.23         8.48         9.63        11.28        11.05 
TCGA-Q2-A5QZ 
       14.07 

$`17P LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
      109.22        98.33        71.41        28.80        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
      100.87        10.68        87.78        86.10        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
       48.82        21.86        34.29        31.07        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.64        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
       60.92        68.61        46.78        48.36        42.08        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 TCGA-AK-3460 
       48.69        45.93        28.73        22.45        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       28.04         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 
        3.48        28.47        19.00         1.38        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14         3.16         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 
       15.72        46.59         5.52        52.21        45.07        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       10.09        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       11.24        11.90         7.30        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 
       60.33        84.92        90.12        56.94        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.75         0.23         1.25         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       24.66        17.19        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.74         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       13.15        61.68        10.82         5.33        61.97        60.59 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
       13.51        56.91        68.38        11.64        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        20.38        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        6.94        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       61.22        61.51         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
       31.79        23.47        13.41        24.62        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
       11.05        21.24        83.97        49.25        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
        0.59        47.08        58.75        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        57.21        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
       14.63        22.78        62.63        45.96        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        18.21        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
       19.13         0.89        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.99        12.46        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       21.63        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
       61.28        50.40        49.84        26.27        20.12         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.04         7.17         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 
        3.02        40.77        79.86        80.88        51.19        61.02 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       54.90        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            151.96             194.79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            47.010             28.765 
[1] "0.2 - 152.0 (47.0)" "0.1 - 194.8 (28.8)"
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        32       30        25       18
  17P LOSS WILD-TYPE     416       73       165       82
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 32                416
  STAGE II                30                 73
  STAGE III               25                165
  STAGE IV                18                 82
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED    32  32  38   3
  17P LOSS WILD-TYPE 430  91 213  12
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               32                430
  T2               32                 91
  T3               38                213
  T4                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"
                    vv
clus                  N0  N1  N2
  17P LOSS MUTATED    53   4   4
  17P LOSS WILD-TYPE 264  39   2
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               53                264
  N1                4                 39
  N2                4                  2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V6, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    63  15
  17P LOSS WILD-TYPE 479  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     63   15
  17P LOSS WILD-TYPE  479   74
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               63                479
  1               15                 74
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    40  65
  17P LOSS WILD-TYPE 247 507
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     40   65
  17P LOSS WILD-TYPE  247  507
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               40                247
  MALE                 65                507
[1] 2 2
[1] FALSE
D71V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17P LOSS MUTATED                   50                                46
  17P LOSS WILD-TYPE                 16                               478
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17P LOSS MUTATED                                       9
  17P LOSS WILD-TYPE                                   260
D71V9, multiclass
                                       clus
vv                                      17P LOSS MUTATED 17P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  50                 16
  KIDNEY CLEAR CELL RENAL CARCINOMA                   46                478
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                9                260
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V10, continuous
D71V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     2
  17P LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                           9    90
  17P LOSS WILD-TYPE                       107   612
D71V12, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       9                107
  WHITE                                          90                612
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V13, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4  59
  17P LOSS WILD-TYPE  38 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   59
  17P LOSS WILD-TYPE   38  538
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               59                538
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    63  16
  17Q LOSS WILD-TYPE 569 195
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                79                764 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                16                195 
$`17Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8328 TCGA-KL-8329 
       38.07       141.73        23.84       137.06       102.81        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        84.89        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       44.84        86.56        28.11        66.54        24.79        73.91 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8443 
       54.74        62.37       151.96        44.91        47.24        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 
      123.12       129.37        87.91        25.48        65.19       104.52 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
        0.99        52.27        87.12        19.33         2.50        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      115.00        42.35        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       16.67        80.38       103.27        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3374 TCGA-AK-3433 
       63.95        49.08        37.15         4.50        43.20        72.07 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 
       67.20        57.37        40.01        12.13        40.70         3.62 
TCGA-B0-4712 TCGA-B0-4817 TCGA-B0-4836 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4166 
       43.96        33.50        40.70        17.59        32.61         0.43 
TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4994 
       21.21        31.89        11.31        36.39        10.98        43.00 
TCGA-BP-5196 TCGA-CJ-4871 TCGA-CJ-5676 TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-5460 
       33.47        79.66        84.66        66.31         6.77        47.01 
TCGA-CZ-5465 
       47.54 

$`17Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8439 TCGA-KM-8441 
      109.22        98.33        71.41        28.80        23.28        28.80 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 
       51.06        31.33        23.47        25.91         3.55        11.21 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
      100.87        10.68        87.78        86.10        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       36.82        47.21         0.53        39.16        24.16        49.02 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
       48.82        21.86        34.29        31.07        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       55.76        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       20.28        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       10.62       109.91        29.10        84.36        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        46.78        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        31.27        28.04         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73         3.16 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        5.52        52.21        45.07        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
       18.21        21.44        37.22        14.76        79.17       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        54.77        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4799 
       60.95        15.78        48.95        36.53        20.38        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       36.95         6.71        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
       63.62        58.68        60.30        61.22        61.51         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       57.40        58.98        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       24.62        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       65.69        54.61        53.52        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        49.25        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
        4.57        18.81        63.88        72.00        79.89        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       73.35        67.00        53.26        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        10.85        10.22        21.76        57.21        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        15.25        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       75.42        34.85        56.81        54.64        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       38.99        26.43        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X 
       25.58         5.29        16.18        22.49         0.13        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       11.57        18.21        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       15.75         8.28        12.99        12.46         9.63        58.45 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
       76.64        13.55        30.35        25.08        44.61        49.25 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
        2.20        19.56         7.33        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       22.06         2.10        19.23         6.81         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       30.28        26.04        25.35        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        0.95        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        48.62        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       34.82        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.33        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
        5.49        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
       67.17        22.26        21.34        16.34        12.36         0.13 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       17.75        14.07        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       21.93         0.53        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            151.96             194.79 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             52.27              28.39 
[1] "0.4 - 152.0 (52.3)" "0.1 - 194.8 (28.4)"
[1] "hr=" "2"  
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        23       27        18       12
  17Q LOSS WILD-TYPE     425       76       172       88
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 23                425
  STAGE II                27                 76
  STAGE III               18                172
  STAGE IV                12                 88
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17Q LOSS MUTATED    23  28  26   3
  17Q LOSS WILD-TYPE 439  95 225  12
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               23                439
  T2               28                 95
  T3               26                225
  T4                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"
                    vv
clus                  N0  N1  N2
  17Q LOSS MUTATED    43   3   2
  17Q LOSS WILD-TYPE 274  40   4
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               43                274
  N1                3                 40
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    49  10
  17Q LOSS WILD-TYPE 493  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     49   10
  17Q LOSS WILD-TYPE  493   79
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               49                493
  1               10                 79
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    30  50
  17Q LOSS WILD-TYPE 257 522
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30   50
  17Q LOSS WILD-TYPE  257  522
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               30                257
  MALE                 50                522
[1] 2 2
[1] FALSE
D72V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17Q LOSS MUTATED                   50                                30
  17Q LOSS WILD-TYPE                 16                               494
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17Q LOSS MUTATED                                       0
  17Q LOSS WILD-TYPE                                   269
D72V9, multiclass
                                       clus
vv                                      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  50                 16
  KIDNEY CLEAR CELL RENAL CARCINOMA                   30                494
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                0                269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V10, continuous
D72V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     2
  17Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           5    70
  17Q LOSS WILD-TYPE                       111   632
D72V12, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 13
  BLACK OR AFRICAN AMERICAN                       5                111
  WHITE                                          70                632
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V13, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4  39
  17Q LOSS WILD-TYPE  38 558
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4   39
  17Q LOSS WILD-TYPE   38  558
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               39                558
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    83  53
  18P LOSS WILD-TYPE 549 158
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               136                707 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                53                158 
$`18P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8427 TCGA-KN-8429 
      102.81        90.48        98.96        30.25         0.99        87.12 
TCGA-KO-8414 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 
       77.85        37.15         4.50        52.93        88.37        24.16 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 
       20.28       109.91        15.78        67.20        57.37        12.13 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4712 
        1.38         3.62        65.10         5.98        19.73        43.96 
TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        6.64        46.59        52.21         6.02        40.44        36.53 
TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5092 
       29.10        40.70        10.29        65.29        29.03        15.09 
TCGA-B0-5097 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 
       21.86         1.68        21.57         0.23         0.53        25.55 
TCGA-B8-4621 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4164 TCGA-BP-4166 
       25.91        27.02         6.38        14.27        32.61         0.43 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4756 
       93.99        18.48        62.86        11.31        12.33        12.30 
TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4962 
        5.98        10.82        68.38        36.39         6.71        58.68 
TCGA-BP-4977 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
       14.93        31.30        43.00        18.51         6.35        30.64 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       62.86        49.15        31.79        33.47        19.82        34.95 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 
       31.27        63.25        73.22        74.27        66.21        61.91 
TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5677 
       51.52        26.93        47.67        49.28         4.57        25.71 
TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4857 TCGA-CZ-4858 
       22.32        60.99        53.42        66.31        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5468 TCGA-CZ-5984 
        6.77        63.39        61.41        56.28         1.94        67.96 
TCGA-CZ-5985 TCGA-CZ-5988 TCGA-MM-A84U TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ 
       65.65        22.78        15.25        54.64        51.52        35.67 
TCGA-2Z-A9JP TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A57E TCGA-AL-A5DJ 
       29.36        12.82        18.21        25.64         8.48        49.25 
TCGA-B1-7332 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 
        7.33         0.46        10.09        20.61         8.88        22.92 
TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7058 
       21.63        25.35         2.76       123.62        93.34        11.28 
TCGA-BQ-7059 TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
        7.63         3.75        24.89        10.68        13.08         4.01 
TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVL 
       12.92         3.68         2.04         0.13         6.61        16.01 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-Y8-A8S1 
       14.07        11.93        38.63        13.28 

$`18P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 
       38.07       141.73        23.84       109.22       137.06       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.11        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        3.55        52.27        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       86.10        57.17        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.02        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 
       37.38        48.82        21.86        34.29        31.07        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       29.92        18.44        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        53.29        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ 
       20.71        18.64        18.87        28.31        65.52        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       22.65         0.10         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       84.36        73.08        66.31        60.92        72.07        68.61 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
       46.78        48.36        42.08        40.01        58.49        48.69 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       45.93        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       28.04        40.70         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4706 
        2.53         3.48        28.47        19.00         7.82         2.14 
TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 
        3.16         3.25        20.25        15.72         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 
       45.07        33.50        16.77        14.93        54.48        10.09 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       56.68        11.64        39.45        26.07         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
       25.32        18.51        10.95         8.05         2.24        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 
       16.67         9.57         5.75         1.25         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       25.05        24.66        17.19        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 
        1.18         0.85        24.23        17.16        16.60         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
       34.39        14.30        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
       99.85        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        74.17        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       31.89        33.99        31.33        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        5.33        61.97        60.59        13.51        56.91        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        20.38        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
       37.25        36.95        47.97         6.94        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       63.62        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
       47.11        53.65        36.07        33.34        46.45        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       45.07        30.64        41.62        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 
       37.48        35.21        36.23        28.87        48.10        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
        1.78        74.20        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 
       33.24        23.47        13.41        24.62        44.55         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       59.84        46.55        14.17        75.88        65.69        54.61 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       53.52        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        75.06        77.36        64.27        71.87 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        69.86        64.18        30.64        63.98        68.55 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
       56.35        49.97        51.29        58.92        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 
       54.48        38.56        45.14         3.06        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
       72.00        79.89        84.66        18.87        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 
       61.91        62.10        73.35        67.00        53.26        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
        5.39        85.78        73.18        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4864 TCGA-CZ-4865 
        0.59        58.75        14.66        60.59        93.04         5.46 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82         0.82        23.74        18.44        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 
       57.21        47.54        22.52         2.40        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       80.19        12.26        14.63        62.63        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
       65.88        12.16        11.67        37.15        66.28        56.84 
TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        66.02        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        7.96        10.29        70.13        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        10.85         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
      100.27        56.91         4.57        67.30        75.42        34.85 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y 
       25.58         5.29        16.18        22.49         0.13        11.57 
TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       19.63        61.05         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        29.46        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       23.31         0.76        19.63        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
       16.96        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       44.61         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
        3.55        16.77         6.58        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       12.46        10.16        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
        1.15        15.12        43.99        22.06         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        6.81         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
       19.27        63.72        43.20        47.80        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       30.28        26.04        13.25        10.88         7.66         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7050 
       11.97         7.92        48.26        96.92        44.84        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 
       50.40        49.84        26.27        20.12         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
       24.46        13.78        14.63         3.02        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 
       17.98        17.33        16.90        80.65       194.79        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        67.17        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       21.34        16.34        12.36        11.97        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94        84.95        92.58        52.27        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       86.27        38.86        52.11        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
       12.99        26.01        29.00        18.64        15.91        18.64 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.05        15.62        25.28         6.74         6.02 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.13               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.62             194.79 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            25.595             31.270 
[1] "0.1 - 123.6 (25.6)" "0.1 - 194.8 (31.3)"
[1] "hr=" "2"  
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        45       11        50       29
  18P LOSS WILD-TYPE     403       92       140       71
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 45                403
  STAGE II                11                 92
  STAGE III               50                140
  STAGE IV                29                 71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P LOSS MUTATED    47  15  69   6
  18P LOSS WILD-TYPE 415 108 182   9
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               47                415
  T2               15                108
  T3               69                182
  T4                6                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18P LOSS MUTATED    53  12   3
  18P LOSS WILD-TYPE 264  31   3
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               53                264
  N1               12                 31
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V6, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    91  24
  18P LOSS WILD-TYPE 451  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     91   24
  18P LOSS WILD-TYPE  451   65
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               91                451
  1               24                 65
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    48  91
  18P LOSS WILD-TYPE 239 481
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     48   91
  18P LOSS WILD-TYPE  239  481
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               48                239
  MALE                 91                481
[1] 2 2
[1] FALSE
D73V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18P LOSS MUTATED                    8                                93
  18P LOSS WILD-TYPE                 58                               431
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18P LOSS MUTATED                                      38
  18P LOSS WILD-TYPE                                   231
D73V9, multiclass
                                       clus
vv                                      18P LOSS MUTATED 18P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   8                 58
  KIDNEY CLEAR CELL RENAL CARCINOMA                   93                431
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               38                231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V10, continuous
D73V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     5
  18P LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          13   118
  18P LOSS WILD-TYPE                       103   584
D73V12, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           5                 10
  BLACK OR AFRICAN AMERICAN                      13                103
  WHITE                                         118                584
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V13, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  93
  18P LOSS WILD-TYPE  39 504
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   93
  18P LOSS WILD-TYPE   39  504
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               93                504
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    88  55
  18Q LOSS WILD-TYPE 544 156
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               143                700 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                55                156 
$`18Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 TCGA-KN-8424 TCGA-KN-8427 
      102.81        90.48        98.96        30.25        65.19         0.99 
TCGA-KN-8429 TCGA-KO-8404 TCGA-KO-8414 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3346 
       87.12        10.68        77.85        24.16        37.15         4.50 
TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3430 
       52.93        88.37        24.16        20.28       109.91        15.78 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
       67.20        57.37        12.13         1.38         3.62        65.10 
TCGA-B0-4703 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4815 TCGA-B0-4819 TCGA-B0-4821 
        5.98        43.96         6.64        52.21         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 
       36.53        29.10        40.70        10.29        65.29        29.03 
TCGA-B0-5092 TCGA-B0-5097 TCGA-B0-5121 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 
       15.09        21.86        18.21         1.68        21.57         0.23 
TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 
        0.53        25.55        25.91        27.02         6.38        14.27 
TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4353 
       32.61         0.43        93.99        62.86        11.31        12.33 
TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 
       12.30         5.98        10.82        68.38        36.39         6.71 
TCGA-BP-4962 TCGA-BP-4977 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 
       58.68        14.93        31.30        43.00        18.51         6.35 
TCGA-BP-5175 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5191 TCGA-BP-5196 
       30.64        62.86        49.15        38.30        31.79        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4872 
       19.82        34.95        31.27        63.25        73.22        47.18 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4891 TCGA-CJ-4901 TCGA-CJ-4907 
       74.27        66.21        51.52        26.93        47.67        49.28 
TCGA-CJ-4920 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6032 
        4.57        25.71        22.32        60.99        53.42        83.77 
TCGA-CW-5588 TCGA-CZ-4854 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4863 
       66.31        46.16        47.08        69.21         6.77        63.39 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5988 
       61.41        56.28         1.94        67.96        65.65        22.78 
TCGA-MM-A84U TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JP TCGA-4A-A93X 
       15.25        54.64        51.52        35.67        29.36        12.82 
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 
       18.21        25.64         8.48        12.99        49.25         7.33 
TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
        0.46        10.09        20.61         8.88        22.92        21.63 
TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7058 TCGA-BQ-7059 
       25.35         2.76       123.62        93.34        11.28         7.63 
TCGA-DW-7840 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 
        3.75        24.89        10.68        13.08         0.43         4.01 
TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA 
       16.90        12.92         3.68         2.04         0.13         6.61 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       14.07        11.93        38.63        86.27        13.28 

$`18Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8330 
       38.07       141.73        23.84       109.22       137.06       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 
       84.89        98.33        96.95        92.55        44.84        86.56 
TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       28.11        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       54.74        62.37       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       47.24        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       23.47        87.91        25.48        25.91       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       52.27        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87        76.90        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8415 
       16.67        80.38        87.78       103.27        86.10        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
        0.53        39.16        49.08        49.02        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3358 
       34.29        31.07        45.53        29.92        18.44        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       28.31        65.52        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
       11.18        10.62        29.10        84.36        73.08        66.31 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       60.92        72.07        68.61        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       40.01        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 
       37.58        38.40        31.27        28.04        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4714 
       19.00         7.82         2.14        19.73         3.16         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       20.25        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 
       33.50        16.77        14.93        54.48        10.09        78.44 
TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       68.71        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       11.64        39.45        26.07         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5088 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 
       18.51        10.95         8.05         2.24        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        35.90        11.80        26.20        21.60        17.59 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
        1.94        16.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       61.32        97.41        32.61        35.90        12.30        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        11.77        10.36        32.98        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        5.75         1.25         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 
       17.19        23.01        20.91        23.74         1.18         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       24.23        17.16        16.60         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
       27.29        29.88        17.06         1.74         8.42         4.93 
TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 
       17.36        15.42        16.27        14.17       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
       94.72        90.28       101.06        93.34        99.85        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 
       37.25        21.21        15.16         0.07        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       74.17        54.77        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4762 
       33.99        31.33        72.59        77.98        77.62        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
       61.97        60.59        13.51        56.91        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        20.38        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
       53.65        36.07        33.34        46.45        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 
       35.21        36.23        28.87        48.10        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 
       74.20        52.27         9.63        74.40        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
       37.22        22.78        13.35        27.02        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       13.41        24.62        44.55         0.95        59.84        46.55 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 
       11.05        21.24        83.97        49.25        79.66        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       77.36        64.27        71.87        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       64.18        30.64        63.98        68.55        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       27.65        39.45        59.44        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        58.92        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       84.66        18.87        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6033 
       73.35        67.00        53.26        75.58        62.66         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
       78.18        74.66         1.35       105.93        83.90       103.43 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
       18.77        25.45         0.59        58.75        14.66        60.59 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04         5.46        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        57.21        47.54        22.52         2.40 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
       31.10        12.69        80.19        12.26        14.63        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
        2.01        19.43        19.96        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       75.42        34.85        56.81        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       24.33        31.20        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
        0.13        11.57        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       14.33        12.46        16.96        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
       12.46         9.63        58.45        76.64        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
       25.08        44.61         2.20        19.56        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
       16.87         3.55        16.77         6.58        33.83        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       34.49        12.46        10.16        50.50        28.18        26.40 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
        0.46         1.15        15.12        43.99        22.06         2.10 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       19.23         6.81         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       86.76        19.27        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
       26.04        30.28        26.04        13.25        10.88         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7049 
        0.95        11.97         7.92        48.26        96.92        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7060 
       61.28        50.40        49.84        26.27        20.12         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       37.55        24.46        13.78        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
       19.00         2.40         1.18        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM 
       17.98        17.33        80.65       194.79        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
       12.43        17.95         0.89        11.21         4.60        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       13.41        11.84        56.75        73.25         5.49        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        67.17        22.26        21.34 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       16.34        12.36        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       43.76        18.02        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       15.62        25.28         6.74         6.02 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.13               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            123.62             194.79 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            25.640             31.235 
[1] "0.1 - 123.6 (25.6)" "0.1 - 194.8 (31.2)"
[1] "hr=" "2"  
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        50       12        51       30
  18Q LOSS WILD-TYPE     398       91       139       70
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 50                398
  STAGE II                12                 91
  STAGE III               51                139
  STAGE IV                30                 70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q LOSS MUTATED    53  17  68   7
  18Q LOSS WILD-TYPE 409 106 183   8
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               53                409
  T2               17                106
  T3               68                183
  T4                7                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  18Q LOSS MUTATED    58  15   3
  18Q LOSS WILD-TYPE 259  28   3
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               58                259
  N1               15                 28
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V6, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    94  24
  18Q LOSS WILD-TYPE 448  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     94   24
  18Q LOSS WILD-TYPE  448   65
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               94                448
  1               24                 65
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    49  97
  18Q LOSS WILD-TYPE 238 475
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     49   97
  18Q LOSS WILD-TYPE  238  475
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               49                238
  MALE                 97                475
[1] 2 2
[1] FALSE
D74V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18Q LOSS MUTATED                   10                                95
  18Q LOSS WILD-TYPE                 56                               429
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18Q LOSS MUTATED                                      41
  18Q LOSS WILD-TYPE                                   228
D74V9, multiclass
                                       clus
vv                                      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  10                 56
  KIDNEY CLEAR CELL RENAL CARCINOMA                   95                429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               41                228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V10, continuous
D74V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     6
  18Q LOSS WILD-TYPE                                2     9
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          14   123
  18Q LOSS WILD-TYPE                       102   579
D74V12, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           6                  9
  BLACK OR AFRICAN AMERICAN                      14                102
  WHITE                                         123                579
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V13, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3  99
  18Q LOSS WILD-TYPE  39 498
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3   99
  18Q LOSS WILD-TYPE   39  498
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               99                498
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    15  11
  19P LOSS WILD-TYPE 617 200
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                26                817 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                11                200 
$`19P LOSS MUTATED`
TCGA-KO-8415 TCGA-A3-3319 TCGA-AK-3425 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4707 
       57.17        37.15       109.91         1.41        28.47        19.73 
TCGA-B0-4828 TCGA-BP-4164 TCGA-BP-4770 TCGA-BP-4985 TCGA-CZ-4860 TCGA-2Z-A9JG 
       10.09        32.61        10.82        31.30         6.77        54.64 
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5876 
       18.21        25.64        12.99         7.33         2.10        19.27 
TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-P4-A5EB 
        0.95         4.01        25.84        16.90         2.04        84.95 
TCGA-Q2-A5QZ TCGA-UZ-A9PN 
       14.07        21.93 

$`19P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 
      151.96        23.28        44.91        28.80        47.24        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       25.48        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       86.10        77.85        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
       49.02        49.58        48.59        36.36        38.99        24.69 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 
       37.38        48.82        21.86        34.29        31.07         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
       52.93        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
        0.10         0.10        11.18        10.62        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        3.32         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.62        65.10         7.82         5.98         2.14         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 
       43.30        11.24        11.90         7.30        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       17.59         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       14.76        79.17       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       17.19        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
        1.18        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        14.27         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
       29.88        17.06         1.74         8.42         4.93        17.36 
TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
       15.42        16.27        14.17       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       97.45        53.42         3.58        27.78        62.07        80.68 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       37.25        21.21        15.16         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       87.45        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        46.45        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       62.86        74.40        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       27.65        39.45        59.44        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       67.00        53.26        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JI 
        4.57        67.30        75.42        34.85        56.81        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       12.82        11.57        19.63        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       23.97        23.28        23.31         0.76        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       14.33        12.46        16.96         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
        8.28        12.46         9.63        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        6.58        33.83        10.09        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
        1.15        15.12        43.99        22.06        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        86.76         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66        11.97         7.92         2.76       123.62        48.26 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
       96.92        93.34        44.84        61.28        50.40        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        3.81        11.61        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
       79.86        80.88        51.19        61.02        54.90        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        48.62        11.05        39.25        34.82 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        13.68         6.38        17.98        17.33        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
       17.95         0.89        11.21         4.60        68.12        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
       85.78        88.24        67.17        22.26        21.34        16.34 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36         0.13        11.97        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
       27.78        30.38        27.65        20.25         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       25.97        21.44        15.48        99.78        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
        6.61        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       12.85        17.75        47.90        47.44        33.04        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       27.06        11.93        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        48.30        43.76        18.02        60.03        14.83 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
        0.53        86.27        38.86        52.11        30.67        25.68 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
       27.39        12.99        26.01        29.00        18.64        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       18.64        18.05        15.62        25.28         6.74         6.02 
TCGA-Y8-A8S1 
       13.28 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.95               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
            109.91             194.79 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             18.74              30.71 
[1] "0.9 - 109.9 (18.7)" "0.1 - 194.8 (30.7)"
[1] "hr=" "2.6"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         7        1        12        5
  19P LOSS WILD-TYPE     441      102       178       95
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  7                441
  STAGE II                 1                102
  STAGE III               12                178
  STAGE IV                 5                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P LOSS MUTATED     8   2  13   3
  19P LOSS WILD-TYPE 454 121 238  12
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                8                454
  T2                2                121
  T3               13                238
  T4                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"
                    vv
clus                  N0  N1  N2
  19P LOSS MUTATED     7   3   1
  19P LOSS WILD-TYPE 310  40   5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                7                310
  N1                3                 40
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V6, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    10   3
  19P LOSS WILD-TYPE 532  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10    3
  19P LOSS WILD-TYPE  532   86
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               10                532
  1                3                 86
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     8  18
  19P LOSS WILD-TYPE 279 554
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      8   18
  19P LOSS WILD-TYPE  279  554
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                8                279
  MALE                 18                554
[1] 2 2
[1] FALSE
D75V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19P LOSS MUTATED                    1                                10
  19P LOSS WILD-TYPE                 65                               514
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19P LOSS MUTATED                                      15
  19P LOSS WILD-TYPE                                   254
D75V9, multiclass
                                       clus
vv                                      19P LOSS MUTATED 19P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   1                 65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   10                514
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               15                254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V10, continuous
D75V11, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 65 
        TCGA-KL-8330         TCGA-KL-8335         TCGA-KL-8341 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8433 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-KO-8408         TCGA-KO-8409         TCGA-A3-A8OV 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-5158 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A563 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MM-A84U         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9J8         TCGA-2Z-A9JD         TCGA-2Z-A9JI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-4A-A93W 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-A4-A48D         TCGA-A4-A57E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3472         TCGA-AL-7173 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4117         TCGA-B9-A69E 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7963         TCGA-F9-A97G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LE 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-SX-A7SS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PM         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     0
  19P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           3    23
  19P LOSS WILD-TYPE                       113   679
D75V12, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       3                113
  WHITE                                          23                679
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V13, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  19
  19P LOSS WILD-TYPE  41 578
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   19
  19P LOSS WILD-TYPE   41  578
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               19                578
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    14   8
  19Q LOSS WILD-TYPE 618 203
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                22                821 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 8                203 
$`19Q LOSS MUTATED`
TCGA-KL-8341 TCGA-KN-8427 TCGA-KO-8415 TCGA-A3-3319 TCGA-B0-4690 TCGA-BP-4164 
       24.79         0.99        57.17        37.15         1.41        32.61 
TCGA-CZ-4860 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A5Y1 
        6.77        54.64        51.52        18.21        25.64        12.99 
TCGA-B1-7332 TCGA-B9-A44B TCGA-BQ-5891 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-7502 
        7.33         2.10         0.95        10.68         4.01        25.84 
TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Q2-A5QZ TCGA-UZ-A9PN 
       16.90         2.04        14.07        21.93 

$`19Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       92.55        30.25        44.84        86.56        28.11        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 
       23.28        44.91        28.80        47.24        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 
       25.91        65.19       104.52         3.55        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87        76.90        10.68        74.93        79.04        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 
       16.67        80.38        87.78       103.27        86.10        77.85 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        0.53        39.16        24.16        49.08        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       43.20        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        4.57         2.53         3.48        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.62        65.10         7.82         5.98         2.14        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       16.77         6.02        40.44        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       85.51        94.72        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       64.27        54.90        97.45        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       62.07        80.68        37.25        21.21        15.16         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 
       93.99        18.48        52.24        74.17        62.86        54.77 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
       49.08        44.94        12.23        31.89        11.31        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       16.47         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       49.15        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75        14.66        60.59        63.39        93.04 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       45.96        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        66.02        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 
        4.18         7.96        10.29        70.13        35.87         2.01 
TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        15.25        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        67.30 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       75.42        34.85        56.81        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 
       16.18        22.49         0.13        12.82        11.57        19.63 
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       61.05         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        29.46        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 
        8.48        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
       49.25         2.20        19.56        21.67        24.56        16.87 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
        3.55        16.77         0.46         6.58        33.83        10.09 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5892 
       26.04        25.35        13.25        10.88         7.66        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
        7.92         2.76       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
       11.28         7.63         7.04         7.17         3.81        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        3.75        14.63         3.02        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       51.19        61.02        54.90        34.19        19.00        24.89 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        48.62 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        34.82        25.15        13.68         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        17.33        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
       27.65         1.05        12.43        17.95         0.89        11.21 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
        4.60        68.12        13.41        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
        5.49        16.80        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
       20.25         0.36        12.13        25.97        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.22        42.94         6.61        84.95        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       52.27        16.01        50.60        78.90        12.85        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        47.44        33.04        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       19.00        38.63        16.31        41.62        26.47        48.30 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       43.76        18.02        60.03        14.83         0.53        86.27 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.95               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             57.17             194.79 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            15.485             30.710 
[1] "0.9 - 57.2 (15.5)"  "0.1 - 194.8 (30.7)"
[1] "hr=" "2.9"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         4        1        11        5
  19Q LOSS WILD-TYPE     444      102       179       95
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  4                444
  STAGE II                 1                102
  STAGE III               11                179
  STAGE IV                 5                 95
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q LOSS MUTATED     5   1  13   3
  19Q LOSS WILD-TYPE 457 122 238  12
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                5                457
  T2                1                122
  T3               13                238
  T4                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"
                    vv
clus                  N0  N1  N2
  19Q LOSS MUTATED     3   4   2
  19Q LOSS WILD-TYPE 314  39   4
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                3                314
  N1                4                 39
  N2                2                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V6, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     5   2
  19Q LOSS WILD-TYPE 537  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    2
  19Q LOSS WILD-TYPE  537   87
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                5                537
  1                2                 87
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  14
  19Q LOSS WILD-TYPE 279 558
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   14
  19Q LOSS WILD-TYPE  279  558
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                279
  MALE                 14                558
[1] 2 2
[1] FALSE
D76V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19Q LOSS MUTATED                    3                                 4
  19Q LOSS WILD-TYPE                 63                               520
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19Q LOSS MUTATED                                      15
  19Q LOSS WILD-TYPE                                   254
D76V9, multiclass
                                       clus
vv                                      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   3                 63
  KIDNEY CLEAR CELL RENAL CARCINOMA                    4                520
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               15                254
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V10, continuous
D76V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4    17
  19Q LOSS WILD-TYPE                       112   685
D76V12, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       4                112
  WHITE                                          17                685
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V13, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  15
  19Q LOSS WILD-TYPE  41 582
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   15
  19Q LOSS WILD-TYPE   41  582
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               15                582
[1] 2 2
[1] FALSE

Clustering(77) Variable = 20P LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED     7   5
  20P LOSS WILD-TYPE 625 206
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                831 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                206 
$`20P LOSS MUTATED`
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KN-8434 TCGA-B0-4821 TCGA-BP-4352 
       92.55        30.25        86.56        59.08        40.44        11.31 
TCGA-BP-4962 TCGA-BP-5000 TCGA-BP-5182 TCGA-BP-5184 TCGA-CJ-4637 TCGA-BQ-5879 
       58.68        18.51        38.30        37.25        73.22        22.92 

$`20P LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8337 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
        2.50        11.21       115.00        42.35       100.87        76.90 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68        74.93        79.04        92.71        16.67        80.38 
TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       87.78       103.27        86.10        77.85        57.17        61.58 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       39.16        24.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       21.86        34.29        31.07         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
       29.92        18.44        88.37        42.97        82.32        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
       43.20        55.76        20.71        18.64        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       65.52        20.28        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 
       11.18        10.62       109.91        29.10        84.36        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
       66.31        15.78        60.92        72.07        68.61        67.20 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       57.37        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       29.10        10.09        78.44        68.71        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        11.64        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       26.20        21.60        17.59         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       21.44        37.22        14.76        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
      102.48        47.97        96.36        89.49        61.32        97.41 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       20.91        23.74         1.18        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
       14.30        27.29        29.88        17.06         1.74         8.42 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 
        4.93        17.36        15.42        16.27        14.17       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 
       61.78        64.27        54.90        97.45        53.42         3.58 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       27.78        62.07        80.68        37.25        21.21        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4353 
       54.77        49.08        44.94        12.23        31.89        12.33 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       33.99        31.33        12.30        72.59        77.98        77.62 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        6.71        47.97         6.94        87.45        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 
        5.82        43.00        45.07        30.64        41.62        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 
       52.27         9.63        62.86        74.40        49.15        42.44 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 
       14.17        75.88        65.69        54.61        53.52        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45        59.44        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       53.26        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       83.90       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        47.01        10.85        10.22        21.76        57.21 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
       62.63        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 
       37.15        66.28        56.84        23.90        66.02        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 
        3.91         6.77         4.18         7.96        10.29        70.13 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
       35.87         2.01        19.43        19.96        15.25        10.85 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN 
       51.52        35.67        38.99        26.43        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT 
       31.20        29.36        25.58         5.29        16.18        22.49 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 
        0.13        12.82        11.57        18.21        19.63        61.05 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
        0.76        19.63        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
        8.48        16.31        15.75         8.28        12.99        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        9.63        58.45        76.64        13.55        30.35        25.08 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
       44.61        49.25         2.20        19.56         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       24.56        16.87         3.55        16.77         0.46         6.58 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
       33.83        10.09        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
       15.12        43.99        22.06         2.10        19.23         6.81 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             11.31               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             92.55             194.79 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             39.37              30.38 
[1] "11.3 - 92.5 (39.4)" "0.1 - 194.8 (30.4)"
[1] "hr=" "1.3"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         3        2         4        3
  20P LOSS WILD-TYPE     445      101       186       97
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                445
  STAGE II                 2                101
  STAGE III                4                186
  STAGE IV                 3                 97
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P LOSS MUTATED     3   3   6   0
  20P LOSS WILD-TYPE 459 120 245  15
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                459
  T2                3                120
  T3                6                245
  T4                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"
                    vv
clus                  N0  N1  N2
  20P LOSS MUTATED     5   1   1
  20P LOSS WILD-TYPE 312  42   5
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                5                312
  N1                1                 42
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     9   2
  20P LOSS WILD-TYPE 533  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    2
  20P LOSS WILD-TYPE  533   87
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                9                533
  1                2                 87
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     6   6
  20P LOSS WILD-TYPE 281 566
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    6
  20P LOSS WILD-TYPE  281  566
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                6                281
  MALE                  6                566
[1] 2 2
[1] FALSE
D77V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20P LOSS MUTATED                    4                                 7
  20P LOSS WILD-TYPE                 62                               517
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                   268
D77V9, multiclass
                                       clus
vv                                      20P LOSS MUTATED 20P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                    7                517
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                268
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V10, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 90 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8341 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8416         TCGA-A3-A8CQ         TCGA-A3-A8OV 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-4621 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JK         TCGA-2Z-A9JM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-2Z-A9JQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-8310 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4115         TCGA-B9-4117 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A69E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7963 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DD         TCGA-HE-A5NI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IZ-A6M8         TCGA-MH-A854 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D77V11, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 66 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-A3-A8OV         TCGA-A3-A8OW 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-DV-A4W0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0    11
  20P LOSS WILD-TYPE                       116   691
D77V12, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 14
  BLACK OR AFRICAN AMERICAN                       0                116
  WHITE                                          11                691
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V13, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   4
  20P LOSS WILD-TYPE  41 593
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    4
  20P LOSS WILD-TYPE   41  593
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO                4                593
[1] 2 2
[1] FALSE

Clustering(78) Variable = 20Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                  0   1
  20Q LOSS MUTATED     4   2
  20Q LOSS WILD-TYPE 628 209
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                837 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                209 
$`20Q LOSS MUTATED`
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-BP-4962 TCGA-BP-5000 TCGA-CJ-4637 
       92.55        30.25        86.56        58.68        18.51        73.22 

$`20Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8337 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        28.11        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 
       28.80        54.74        62.37       151.96        23.28        44.91 
TCGA-KM-8441 TCGA-KM-8442 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        47.24        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
       76.90        10.68        74.93        79.04        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       80.38        87.78       103.27        86.10        77.85        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 
       61.58        63.95        12.66        12.16        36.82        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.53        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
       49.58        48.59        36.36        38.99        24.69        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 
       48.82        21.86        34.29        31.07         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 
       45.53        29.92        18.44        88.37        42.97        82.32 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       53.29        43.20        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        20.28        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
        0.10        11.18        10.62       109.91        29.10        84.36 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
       73.08        66.31        15.78        60.92        72.07        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       67.20        57.37        46.78        48.36        42.08        40.01 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       58.49        48.69        45.93        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        31.27        28.04        12.13        40.70         1.41 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
        3.32         1.41         4.57         2.53         3.48        28.47 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       19.00         1.38         3.62        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
        2.14        19.73         3.16        43.96         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
       20.25        15.72        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       45.07        33.50        16.77         6.02        40.44        36.53 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
       14.93        54.48        29.10        10.09        78.44        68.71 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.90         7.30        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       35.90        11.80        26.20        21.60        17.59         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       16.21        18.21        21.44        37.22        14.76        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      120.59        79.36       102.48        47.97        96.36        89.49 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       61.32        97.41        32.61        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
       21.30        31.30        11.77        10.36        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67         9.57         5.75         0.23         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
        0.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 
        1.74         8.42         4.93        17.36        15.42        16.27 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.17       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
       53.42         3.58        27.78        62.07        80.68        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.16         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        54.77        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       31.89        11.31        12.33        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       72.59        77.98        77.62         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       71.80        48.07        13.15        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       61.97        60.59        13.51        56.91        68.38        11.64 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 
       60.95        15.78        48.95        36.53        20.38        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
       87.45        71.41        63.62        60.30        61.22        61.51 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        6.74        57.40        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        3.88        46.45        16.47         5.82        43.00        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       30.64        41.62        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       74.40        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 
       31.27         0.95        59.84        46.55        63.25        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
       75.88        65.69        54.61        53.52        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       59.44        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
       18.15        61.91        62.10        73.35        67.00        53.26 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       66.31        78.18        74.66         1.35       105.93        83.90 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       47.01        10.85        10.22        21.76        57.21        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
       43.69        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 
       66.28        56.84        23.90        66.02        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 
        6.77         4.18         7.96        10.29        70.13        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
        2.01        19.43        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.30        75.42        34.85        56.81        54.64        51.52 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 
       12.82        11.57        18.21        19.63        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 
       16.31        15.75         8.28        12.99        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       58.45        76.64        13.55        30.35        25.08        44.61 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
       49.25         2.20        19.56         7.33        21.67        24.56 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
       16.87         3.55        16.77         0.46         6.58        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
       10.09        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
       28.18        26.40        20.61         0.46         1.15        15.12 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
       43.99        22.06         2.10        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.17         3.81        11.61        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
       40.77        79.86        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        48.62        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        34.82        25.15        13.68        25.84         6.38 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        17.33        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
        0.13        11.97        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
       30.38        27.65        20.25         0.36        12.13        25.97 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       21.44        15.48        99.78        87.22        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       84.95        92.58        52.27        16.01        50.60        78.90 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       12.85        17.75        14.07        47.90        47.44        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP 
       28.80        27.06        11.93        19.00        38.63        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PK 
       41.62        26.47        48.30        43.76        18.02        60.03 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS 
       14.83        21.93         0.53        86.27        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             18.51               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             92.55             194.79 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             65.95              30.48 
[1] "18.5 - 92.5 (66.0)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1.3"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         1        1         2        2
  20Q LOSS WILD-TYPE     447      102       188       98
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                447
  STAGE II                 1                102
  STAGE III                2                188
  STAGE IV                 2                 98
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q LOSS MUTATED     1   2   3   0
  20Q LOSS WILD-TYPE 461 121 248  15
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                461
  T2                2                121
  T3                3                248
  T4                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"
                    vv
clus                  N0  N1  N2
  20Q LOSS MUTATED     2   0   1
  20Q LOSS WILD-TYPE 315  43   5
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                315
  N1                0                 43
  N2                1                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V6, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     5   1
  20Q LOSS WILD-TYPE 537  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    1
  20Q LOSS WILD-TYPE  537   88
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                5                537
  1                1                 88
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   4
  20Q LOSS WILD-TYPE 285 568
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    4
  20Q LOSS WILD-TYPE  285  568
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                285
  MALE                  4                568
[1] 2 2
[1] FALSE
D78V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20Q LOSS MUTATED                    3                                 3
  20Q LOSS WILD-TYPE                 63                               521
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                   269
D78V9, multiclass
                                       clus
vv                                      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   3                 63
  KIDNEY CLEAR CELL RENAL CARCINOMA                    3                521
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                0                269
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V10, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 90 
        TCGA-KL-8324         TCGA-KL-8330         TCGA-KL-8341 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8345         TCGA-KM-8639         TCGA-KN-8428 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8433         TCGA-KO-8408         TCGA-KO-8409 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8416         TCGA-A3-A8CQ         TCGA-A3-A8OV 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A3-A8OW         TCGA-B2-A4SR         TCGA-B8-4621 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-A54E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B8-A54F         TCGA-B8-A54G         TCGA-B8-A8YJ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DV-A4W0         TCGA-G6-A5PC         TCGA-G6-A8L7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-2Z-A9J2         TCGA-2Z-A9J5 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         TCGA-2Z-A9JD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JI         TCGA-2Z-A9JK         TCGA-2Z-A9JM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JN         TCGA-2Z-A9JO         TCGA-2Z-A9JQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-8310 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-AL-3472         TCGA-AL-7173 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B1-A654         TCGA-B9-4115         TCGA-B9-4117 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B9-7268         TCGA-B9-A44B         TCGA-B9-A69E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DW-5561         TCGA-DW-7834         TCGA-DW-7963 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-7501         TCGA-G7-A8LB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GL-A59T         TCGA-GL-A9DD         TCGA-HE-A5NI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IZ-A6M8         TCGA-MH-A854 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E7         TCGA-P4-A5EB 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-UZ-A9PS 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D78V11, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 66 
        TCGA-KL-8330         TCGA-KL-8341         TCGA-KL-8345 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8433         TCGA-KO-8408 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-A3-A8OV         TCGA-A3-A8OW 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-DV-A4W0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G6-A8L7         TCGA-MM-A563         TCGA-MM-A84U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J3         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JI         TCGA-2Z-A9JN 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JO         TCGA-4A-A93W         TCGA-4A-A93Y 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A57E         TCGA-A4-A5Y0 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AL-3472         TCGA-AL-7173         TCGA-B1-A654 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-5561 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-7501 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-PJ-A5Z9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71S         TCGA-SX-A71U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UZ-A9PM         TCGA-UZ-A9PO 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PR         TCGA-UZ-A9PS         TCGA-UZ-A9PX 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-WN-A9G9         TCGA-WN-AB4C         TCGA-Y8-A894 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY         TCGA-Y8-A8RZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     6
  20Q LOSS WILD-TYPE                       116   696
D78V12, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 15
  BLACK OR AFRICAN AMERICAN                       0                116
  WHITE                                           6                696
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V13, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   0
  20Q LOSS WILD-TYPE  41 597
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   41  597
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO                0                597
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    97  30
  21Q LOSS WILD-TYPE 535 181
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               127                716 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                30                181 
$`21Q LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8330 TCGA-KL-8331 
       38.07       141.73        23.84       102.81       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 
       84.89        96.95        30.25        86.56        28.11        66.54 
TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8443 TCGA-KM-8476 
       24.79        71.41        28.80        62.37        49.97       123.12 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       25.48        65.19       104.52         0.99        52.27        87.12 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8408 TCGA-KO-8409 
        2.50        59.08        76.90        79.04        16.67        80.38 
TCGA-KO-8411 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-A3-3317 TCGA-A3-3374 
      103.27        77.85        57.17        61.58        49.02        43.20 
TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3465 TCGA-AS-3777 
       84.36        15.78        72.07        57.37        12.13        40.70 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4811 
        1.38         3.62        19.73         3.16        43.96        46.59 
TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-5084 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5695 
       10.09        68.71         7.30        17.59        14.76        46.68 
TCGA-B0-5697 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5553 TCGA-BP-4173 TCGA-BP-4325 
       60.33         5.46        17.19        14.30        62.24        97.45 
TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4803 TCGA-BP-4960 
       21.21        18.48        13.15        10.82         6.71        71.41 
TCGA-BP-4983 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5198 TCGA-CJ-4881 TCGA-CJ-4897 
       46.45        43.00         6.35        19.82        66.21        59.44 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4913 TCGA-CJ-4923 TCGA-CJ-5686 
       47.67        51.29        49.28        38.56        18.81        67.00 
TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6087 TCGA-CZ-4860 TCGA-CZ-5457 
       53.26        53.42        66.31         1.35         6.77        55.33 
TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-MM-A563 TCGA-2Z-A9J6 TCGA-2Z-A9JI 
       56.94        47.54        22.52        19.43        56.91        51.52 
TCGA-2Z-A9JM TCGA-2Z-A9JT TCGA-4A-A93X TCGA-A4-7288 TCGA-A4-8516 TCGA-A4-A4ZT 
       30.71        22.49        12.82        61.05         0.76        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3468 TCGA-B3-3925 TCGA-B3-3926 
        8.48        16.31        15.75        76.64        33.83        10.09 
TCGA-B9-4114 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5885 
       28.18         2.10        19.23         6.81        86.76        30.28 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 TCGA-DZ-6134 TCGA-F9-A4JJ 
       10.88         7.66         2.76         7.17        61.02        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 TCGA-GL-A9DC TCGA-HE-A5NF 
       13.08         4.01        34.82         3.68         0.89        68.12 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-PJ-A5Z9 TCGA-UZ-A9PN 
       16.80         2.04        29.10        11.41        17.75        21.93 
TCGA-UZ-A9PP 
        0.53 

$`21Q LOSS WILD-TYPE`
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8333 TCGA-KL-8335 TCGA-KL-8337 
      109.22       137.06        90.48        98.33        92.55        44.84 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 
       73.91        54.74       151.96        23.28        44.91        28.80 
TCGA-KM-8442 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
       47.24        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 
       25.91         3.55        19.33        11.21       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8413 
      100.87        10.68        74.93        92.71        87.78        86.10 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 
       63.95        12.66        12.16        36.82        47.21         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       39.16        24.16        49.08        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       36.36        38.99        24.69        37.38        48.82        21.86 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       34.29        31.07         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        53.29        55.76 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       20.71        18.64        18.87        28.31        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 
      109.91        29.10        73.08        66.31        60.92        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
       67.20        46.78        48.36        42.08        40.01        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       31.27        28.04         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 
        2.53         3.48        28.47        19.00        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        5.98         2.14         6.64         3.25        20.25        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        79.17       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
      101.13        15.78        56.78        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
        1.68        12.30        21.30        31.30        11.77        10.36 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67         9.57         5.75         0.23 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        27.55        25.05        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        27.29        29.88        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 
       61.78        64.27        54.90        53.42         3.58        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        80.68        37.25        15.16         0.07        93.99 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        54.77        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
       12.23        31.89        11.31        12.33        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
       12.30        72.59        77.98        77.62         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        48.07        61.68         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
       60.59        13.51        56.91        68.38        11.64        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 
       15.78        48.95        36.53        20.38        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 
       37.25        36.95        47.97         6.94        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
       58.68        60.30        61.22        61.51         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       58.98        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 
       47.11        53.65        14.93        36.07        33.34        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       48.10        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        9.63        62.86        74.40        49.15        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 
       73.22        14.17        75.88        65.69        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 
       39.45        50.24        56.35        49.97        58.92        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 
       50.33        54.48        45.14         3.06         4.57        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 
       25.25        18.15        61.91        62.10        73.35        60.99 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
       81.83         5.39        85.78        73.18        78.18        74.66 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
      105.93        83.90       103.43        18.77        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        69.21        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5460 
        0.82        23.74        18.44        56.28        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5468 
       10.85        10.22        21.76        57.21         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       14.63        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       66.02        18.12         3.91         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U 
       10.29        70.13        35.87         2.01        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JG 
        4.57        67.30        75.42        34.85        56.81        54.64 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       35.67        38.99        26.43        24.33        31.20        29.36 
TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7286 
       25.58         5.29        16.18         0.13        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         0.89         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 
       23.31        19.63        19.73        14.33        12.46         8.28 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
       12.99        12.46         9.63        58.45        13.55        30.35 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       25.08        44.61        49.25         2.20        19.56         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
        6.58        30.58        34.49        12.46        10.16        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 
       22.06         0.16        14.86        17.49        12.30        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
       40.83        26.04        26.04        25.35        13.25         0.95 
TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 
       11.97         7.92       123.62        48.26        96.92        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
       44.84        61.28        50.40        49.84        26.27        20.12 
TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
       11.28         7.63         7.04         3.81        11.61        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
       14.63         3.02        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       54.90        34.19        19.00        24.89         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 
        0.43        51.78        48.62        11.05        39.25        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       13.68        25.84         6.38        17.98        17.33        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65       194.79        12.92        27.65         1.05        12.43 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       17.95        11.21         4.60        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       73.25         5.49        19.99        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
       22.26        21.34        16.34        12.36         0.13        11.97 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25         0.36 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       12.13        25.97        21.44        15.48        99.78        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        84.95        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       50.60        78.90        12.85        14.07        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
       33.04        28.80        27.06        11.93        19.00        38.63 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        48.30        43.76        18.02 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU 
       60.03        14.83        86.27        38.86        52.11        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       25.68        27.39        12.99        26.01        29.00        18.64 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
       15.91        18.64        18.05        15.62        25.28         6.74 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.53               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            141.73             194.79 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             30.71              30.48 
[1] "0.5 - 141.7 (30.7)" "0.1 - 194.8 (30.5)"
[1] "hr=" "1.1"
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        48       20        40       19
  21Q LOSS WILD-TYPE     400       83       150       81
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 48                400
  STAGE II                20                 83
  STAGE III               40                150
  STAGE IV                19                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q LOSS MUTATED    48  23  52   6
  21Q LOSS WILD-TYPE 414 100 199   9
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               48                414
  T2               23                100
  T3               52                199
  T4                6                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  N0  N1  N2
  21Q LOSS MUTATED    49  12   3
  21Q LOSS WILD-TYPE 268  31   3
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               49                268
  N1               12                 31
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    77  12
  21Q LOSS WILD-TYPE 465  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     77   12
  21Q LOSS WILD-TYPE  465   77
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               77                465
  1               12                 77
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    47  83
  21Q LOSS WILD-TYPE 240 489
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     47   83
  21Q LOSS WILD-TYPE  240  489
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               47                240
  MALE                 83                489
[1] 2 2
[1] FALSE
D79V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  21Q LOSS MUTATED                   35                                54
  21Q LOSS WILD-TYPE                 31                               470
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  21Q LOSS MUTATED                                      41
  21Q LOSS WILD-TYPE                                   228
D79V9, multiclass
                                       clus
vv                                      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  35                 31
  KIDNEY CLEAR CELL RENAL CARCINOMA                   54                470
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               41                228
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V10, continuous
D79V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     3
  21Q LOSS WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                           9   112
  21Q LOSS WILD-TYPE                       107   590
D79V12, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 12
  BLACK OR AFRICAN AMERICAN                       9                107
  WHITE                                         112                590
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V13, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4  84
  21Q LOSS WILD-TYPE  38 513
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   84
  21Q LOSS WILD-TYPE   38  513
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               84                513
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    69  34
  22Q LOSS WILD-TYPE 563 177
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               103                740 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                34                177 
$`22Q LOSS MUTATED`
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8339 TCGA-KM-8438 TCGA-KN-8422 
      108.62        98.96        30.25        28.11       151.96        25.48 
TCGA-KO-8415 TCGA-A3-3347 TCGA-AK-3453 TCGA-AK-3456 TCGA-B0-4707 TCGA-B0-4712 
       57.17        52.93        45.93        37.58        19.73        43.96 
TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5098 TCGA-B0-5116 
       10.09        10.29        15.09        10.95        52.08        21.60 
TCGA-B0-5701 TCGA-B2-4098 TCGA-B8-4143 TCGA-B8-A54E TCGA-BP-4343 TCGA-BP-4768 
       56.94         1.68        23.31        29.88        62.86        13.15 
TCGA-BP-4799 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4992 
       37.25        71.41         6.74        31.30        25.81        16.47 
TCGA-BP-5175 TCGA-BP-5196 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4891 TCGA-CJ-4897 
       30.64        33.47        73.22        65.69        26.93        59.44 
TCGA-CJ-4901 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5457 
       47.67        53.26        53.42        18.77        61.41        55.33 
TCGA-CZ-5461 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-DV-5566 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       10.85         1.94        31.10        45.96        54.64        51.52 
TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 
       12.82        18.21        61.05        29.46        19.63         8.28 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47O TCGA-B3-3925 
       12.99         9.63        49.25         7.33        16.87        33.83 
TCGA-B3-3926 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5879 
       10.09         2.10         6.81        86.76         8.88        22.92 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        30.28         7.66         0.95         2.76       123.62 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 
       61.28        50.40        26.27        20.12         7.17        79.86 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 
       19.00        10.68        13.08         1.18         4.01        11.05 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y 
       25.15        13.68        25.84        17.33         3.68         2.04 
TCGA-J7-8537 TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SL 
        0.13        25.97         6.61        78.90        14.07        27.06 
TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A896 
       11.93        18.02        21.93        86.27        29.00        18.64 
TCGA-Y8-A8RZ 
        6.74 

$`22Q LOSS WILD-TYPE`
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8328 
       38.07       141.73        23.84       109.22       137.06       102.81 
TCGA-KL-8329 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
       90.48        84.89        98.33        96.95        92.55        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8439 TCGA-KM-8440 TCGA-KM-8441 TCGA-KM-8442 
       54.74        62.37        23.28        44.91        28.80        47.24 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 
       87.91        25.91        65.19       104.52         3.55         0.99 
TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
       52.27        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87        76.90        10.68        74.93 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8411 
       79.04        92.71        16.67        80.38        87.78       103.27 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       86.10        77.85        61.58        63.95        12.66        12.16 
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       36.82        47.21         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.02        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
       24.69        37.38        48.82        21.86        34.29        31.07 
TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 
        4.50        45.53        29.92        18.44        88.37        42.97 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       82.32        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       24.16        53.29        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        28.31        65.52        20.28        15.39        22.65 
TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 TCGA-AK-3426 
        0.10         0.10        11.18        10.62       109.91        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
       84.36        73.08        66.31        15.78        60.92        72.07 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61        67.20        57.37        46.78        48.36        42.08 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3458 
       40.01        58.49        48.69        28.73        22.45        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       31.27        28.04        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 
        1.41         4.57         2.53         3.48        28.47        19.00 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
        1.38         3.62        65.10         7.82         5.98         2.14 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        3.16         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        6.02        40.44        36.53        14.93        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       78.44        68.71        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 
       11.24        11.90         7.30        25.32        18.51         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        17.59         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       37.22        14.76        79.17       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       52.77        39.55       120.59        79.36       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
       96.36        89.49        61.32        97.41        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
       12.30        21.30        31.30        11.77        10.36        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67         9.57         5.75         0.23         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        0.53         4.64         5.46         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       27.16        27.55        25.05        24.66        17.19        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
       25.91        23.01        20.91        23.74         1.18        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
        0.53        34.39        14.30        27.29        17.06         1.74 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K TCGA-B8-A7U6 TCGA-B8-A8YJ 
        8.42         4.93        17.36        15.42        16.27        14.17 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 
        3.58        27.78        62.07        80.68        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       15.16         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.62         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       36.53        20.38        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        87.45        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22        61.51        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       36.07        33.34        46.45        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45         5.82        43.00        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 
       74.20        52.27         9.63        62.86        74.40        49.15 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4642 
       46.55        63.25        14.17        75.88        54.61        53.52 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       51.52        63.98        68.55        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       39.45        50.24        56.35        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6030 
       61.91        62.10        73.35        67.00        60.99        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        5.39        85.78        73.18        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        1.35       105.93        83.90       103.43        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
        0.59        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39        93.04         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        56.28        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.22        21.76        57.21        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        2.40        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        65.88        12.16 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 
       11.67        37.15        66.28        56.84        23.90        66.02 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       18.12         3.91         6.77         4.18         7.96        10.29 
TCGA-G6-A8L7 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
       70.13        35.87         2.01        19.43        19.96        15.25 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       10.85         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE 
       56.91         4.57        67.30        75.42        34.85        56.81 
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       35.67        38.99        26.43        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W 
       29.36        25.58         5.29        16.18        22.49         0.13 
TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 
       11.57        19.63         0.10        35.18        19.13         0.89 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
       23.31         0.76        19.73        14.33        12.46        16.96 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        8.48        16.31        15.75        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       13.55        30.35        25.08        44.61         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
       21.67        24.56         3.55        16.77         0.46         6.58 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
       30.58        34.49        12.46        10.16        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       26.40        20.61         0.46         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        19.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       19.27        63.72        43.20        47.80        21.63        40.83 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-5893 
       26.04        25.35        13.25        10.88        11.97         7.92 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7058 
       48.26        96.92        93.34        44.84        49.84        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        7.63         7.04         3.81        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       34.19        24.89         2.40         0.43        51.78        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       39.25        34.82         6.38        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
      194.79        12.92        27.65         1.05        12.43        17.95 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
        0.89        11.21         4.60        68.12        13.41        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25         5.49        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A857 TCGA-O9-A75Z 
       27.65        20.25         0.36        12.13        21.44        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.22        42.94        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        12.85        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ 
       33.04        28.80        19.00        38.63        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP 
       26.47        48.30        43.76        60.03        14.83         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       26.01        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.13               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            151.96             194.79 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             25.48              31.84 
[1] "0.1 - 152.0 (25.5)" "0.1 - 194.8 (31.8)"
[1] "hr=" "1.7"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        33       10        38       19
  22Q LOSS WILD-TYPE     415       93       152       81
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 33                415
  STAGE II                10                 93
  STAGE III               38                152
  STAGE IV                19                 81
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED    39  13  49   1
  22Q LOSS WILD-TYPE 423 110 202  14
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               39                423
  T2               13                110
  T3               49                202
  T4                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"
                    vv
clus                  N0  N1  N2
  22Q LOSS MUTATED    32  15   3
  22Q LOSS WILD-TYPE 285  28   3
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               32                285
  N1               15                 28
  N2                3                  3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V6, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    52  16
  22Q LOSS WILD-TYPE 490  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     52   16
  22Q LOSS WILD-TYPE  490   73
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               52                490
  1               16                 73
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    45  59
  22Q LOSS WILD-TYPE 242 513
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     45   59
  22Q LOSS WILD-TYPE  242  513
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               45                242
  MALE                 59                513
[1] 2 2
[1] FALSE
D80V8, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  22Q LOSS MUTATED                    8                                39
  22Q LOSS WILD-TYPE                 58                               485
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  22Q LOSS MUTATED                                      57
  22Q LOSS WILD-TYPE                                   212
D80V9, multiclass
                                       clus
vv                                      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   8                 58
  KIDNEY CLEAR CELL RENAL CARCINOMA                   39                485
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               57                212
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V10, continuous
D80V11, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     3
  22Q LOSS WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          17    82
  22Q LOSS WILD-TYPE                        99   620
D80V12, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 12
  BLACK OR AFRICAN AMERICAN                      17                 99
  WHITE                                          82                620
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V13, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    10  68
  22Q LOSS WILD-TYPE  32 529
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   68
  22Q LOSS WILD-TYPE   32  529
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 32
  NOT HISPANIC OR LATINO               68                529
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    79  35
  XP LOSS WILD-TYPE 553 176
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              114               729 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               35               176 
$`XP LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07        23.84       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 
       86.56        28.11        66.54        73.91        71.41        54.74 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        47.24       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
       65.19        87.12        19.33         2.50        59.08       115.00 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 
       76.90        79.04        92.71        16.67       103.27        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3383 
       61.58        63.95        36.82        37.15         4.50        28.31 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4699 
       57.37        40.01        12.13        40.70        28.47         3.62 
TCGA-B0-4813 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4845 TCGA-B0-5080 TCGA-B0-5084 
        0.59        68.71        40.70        65.29        11.24         7.30 
TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 TCGA-B8-5159 
       52.08        17.59        14.76       120.59        32.61        23.74 
TCGA-B8-5549 TCGA-B8-A54D TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4334 TCGA-BP-4761 
        6.38        27.29        32.61         3.58        21.21         5.98 
TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5196 TCGA-CJ-4642 
       87.45        37.02        52.27        74.40        33.47        53.52 
TCGA-CJ-4894 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CW-6090 TCGA-CZ-5458 
       27.65        25.71        25.25        60.99        83.90        56.94 
TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-MM-A563 
       47.54        65.65        14.63         4.18        35.87        19.43 
TCGA-MM-A84U TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 
       15.25        67.30        54.64        51.52        12.82        18.21 
TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 
       19.63        12.99         9.63         7.33        10.09        20.61 
TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
       15.12         2.10        19.27         8.88        22.92        21.63 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 
       13.61        79.86        10.68        13.08         0.43        11.05 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       13.68        16.90         0.13        14.07        18.02        86.27 

$`XP LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      141.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
      151.96        23.28        28.80        49.97        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       23.47        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 
       11.21        42.35       100.87        10.68        74.93        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
       87.78        86.10        77.85        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        0.53        39.16        24.16        49.08        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       21.86        34.29        31.07        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.64        18.87        65.52        20.28 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       15.39        22.65         0.10         0.10        11.18        10.62 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
      109.91        29.10        84.36        73.08        66.31        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       60.92        72.07        68.61        67.20        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 
       42.08        58.49        48.69        45.93        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        31.27        28.04         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 
        1.41         4.57         2.53         3.48        19.00         1.38 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       65.10         7.82         5.98         2.14        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       40.44        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       11.64        10.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 
       36.85        70.52        20.94        43.30        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
        1.94        16.21        18.21        21.44        37.22        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E 
       16.60        14.27         0.53        34.39        14.30        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
       53.42        27.78        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.33        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.62        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
       61.68        10.82         5.33        61.97        60.59        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       56.91        68.38        11.64        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       36.53        20.38        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       60.30        61.22        61.51         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
        5.82        43.00        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       38.70        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        49.15        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       23.47        13.41        24.62        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       68.55        26.93        50.01        24.66        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       50.24        56.35        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       84.66        18.87        22.32        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        53.26        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       83.77         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       85.78        73.18        66.31        78.18        74.66         1.35 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
      105.93       103.43        18.77        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 
       47.08        69.21        58.75         6.77        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       63.39        93.04         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 
        0.82        23.74        18.44        56.28        55.33        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        57.21        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.02        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J1 
       70.13         2.01        19.96        10.85         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J9 
       59.01        58.22       100.27        56.91         4.57        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-2Z-A9JM 
       34.85        56.81        35.67        38.99        26.43        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS 
       24.33        31.20        29.36        25.58         5.29        16.18 
TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7585 
       22.49         0.13        11.57        61.05         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         0.89         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       25.64        23.97        23.28        23.31         0.76        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
       19.73        14.33        12.46        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
       15.75         8.28        12.46        58.45        76.64        13.55 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
       30.35        25.08        44.61        49.25         2.20        19.56 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       21.67        24.56        16.87         3.55        16.77         0.46 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        6.58        33.83        30.58        34.49        12.46        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       50.50        28.18        26.40         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       22.06        19.23         6.81         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       12.30        86.76        63.72        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 
       26.04        30.28        26.04        25.35        13.25        10.88 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
        7.66         0.95        11.97         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 
       48.26        96.92        93.34        44.84        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       49.84        26.27        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
        7.17         3.81        11.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
       24.46        13.78         3.75        14.63         3.02        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       80.88        51.19        61.02        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       24.89         2.40         1.18         4.01        51.78        48.62 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        34.82        25.15        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       17.33        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
        1.05        12.43        17.95         0.89        11.21         4.60 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       68.12        13.41        11.84        56.75        73.25         5.49 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W 
       16.80        19.99         2.04        85.78        88.24        67.17 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
       22.26        21.34        16.34        12.36        11.97        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
        0.36        12.13        25.97        21.44        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.22        42.94         6.61        84.95        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
       16.01        50.60        78.90        12.85        17.75        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       47.44        33.04        28.80        27.06        11.93        19.00 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       38.63        16.31        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       60.03        14.83        21.93         0.53        38.86        52.11 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C 
       30.67        25.68        27.39        12.99        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       18.64        15.91        18.64        18.05        15.62        25.28 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.74         6.02        13.28 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.13              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           129.37            194.79 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            34.67             30.35 
[1] "0.1 - 129.4 (34.7)" "0.1 - 194.8 (30.4)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED        41       22        35       14
  XP LOSS WILD-TYPE     407       81       155       86
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                41               407
  STAGE II               22                81
  STAGE III              35               155
  STAGE IV               14                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XP LOSS MUTATED    41  24  47   2
  XP LOSS WILD-TYPE 421  99 204  13
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              41               421
  T2              24                99
  T3              47               204
  T4               2                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 N0  N1  N2
  XP LOSS MUTATED    40  12   2
  XP LOSS WILD-TYPE 277  31   4
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              40               277
  N1              12                31
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V6, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    67  11
  XP LOSS WILD-TYPE 475  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     67   11
  XP LOSS WILD-TYPE  475   78
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              67               475
  1              11                78
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    44  71
  XP LOSS WILD-TYPE 243 501
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     44   71
  XP LOSS WILD-TYPE  243  501
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              44               243
  MALE                71               501
[1] 2 2
[1] FALSE
D81V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XP LOSS MUTATED                   38                                47
  XP LOSS WILD-TYPE                 28                               477
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XP LOSS MUTATED                                      30
  XP LOSS WILD-TYPE                                   239
D81V9, multiclass
                                       clus
vv                                      XP LOSS MUTATED XP LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 38                28
  KIDNEY CLEAR CELL RENAL CARCINOMA                  47               477
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              30               239
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V10, continuous
D81V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     4
  XP LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          19    87
  XP LOSS WILD-TYPE                        97   615
D81V12, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                11
  BLACK OR AFRICAN AMERICAN                     19                97
  WHITE                                         87               615
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V13, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  71
  XP LOSS WILD-TYPE  40 526
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   71
  XP LOSS WILD-TYPE   40  526
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              71               526
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    78  34
  XQ LOSS WILD-TYPE 554 177
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              112               731 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               34               177 
$`XQ LOSS MUTATED`
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8328 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07        23.84       102.81        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8339 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 
       86.56        28.11        66.54        73.91        71.41        54.74 
TCGA-KM-8440 TCGA-KM-8442 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        47.24       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8435 TCGA-KO-8403 
       65.19        87.12        19.33         2.50       115.00        76.90 
TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8411 TCGA-KO-8415 
       10.68        79.04        92.71        16.67       103.27        57.17 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3382 
       61.58        63.95        36.82        37.15         4.50        18.87 
TCGA-A3-3383 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
       28.31        57.37        42.08        40.01        12.13        40.70 
TCGA-B0-4696 TCGA-B0-4813 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4845 TCGA-B0-5084 
       28.47         0.59        68.71        40.70        65.29         7.30 
TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 TCGA-B8-5159 
       52.08        17.59        14.76       120.59        32.61        23.74 
TCGA-B8-5549 TCGA-B8-A54D TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4334 TCGA-BP-4756 
        6.38        27.29        32.61         3.58        21.21        12.30 
TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5180 TCGA-BP-5196 
        5.98        10.82        87.45        37.02        74.40        33.47 
TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-6027 TCGA-CW-6090 
       53.52        27.65        25.71        25.25        60.99        83.90 
TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-MM-A563 
       47.54        65.65        14.63         4.18        35.87        19.43 
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7287 
       67.30        54.64        51.52        12.82        18.21        19.63 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-5155 TCGA-B9-A44B 
       12.99         9.63         7.33        10.09        15.12         2.10 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-DW-5561 TCGA-DZ-6131 
       19.27         8.88        22.92        21.63        13.61        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LD 
       10.68        13.08         0.43        11.05        13.68        16.90 
TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
        0.13        14.07        18.02        86.27 

$`XQ LOSS WILD-TYPE`
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      141.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 
      151.96        23.28        28.80        49.97        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       23.47        25.91       104.52         3.55         0.99        52.27 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8405 TCGA-KO-8409 
       11.21        59.08        42.35       100.87        74.93        80.38 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3307 
       87.78        86.10        77.85        12.66        12.16        47.21 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 
        0.53        39.16        24.16        49.08        49.02        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
       48.59        36.36        38.99        24.69        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       21.86        34.29        31.07        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
       18.44        88.37        42.97        82.32        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
       28.70        74.63        74.76        24.16        53.29        43.20 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ 
       55.76        20.71        18.64        65.52        20.28        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3425 
       22.65         0.10         0.10        11.18        10.62       109.91 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10        84.36        73.08        66.31        15.78        60.92 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 
       72.07        68.61        67.20        46.78        48.36        58.49 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       48.69        45.93        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       31.27        28.04         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 
        2.53         3.48        19.00         1.38         3.62        65.10 
TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
        7.82         5.98         2.14        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 
        6.64         3.25        20.25        15.72        46.59         5.52 
TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
       52.21        45.07        33.50        16.77         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       10.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 
       70.52        20.94        43.30        11.24        11.90        25.32 
TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       18.51        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       29.95        19.30        35.90        11.80        26.20        21.60 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
        1.94        16.21        18.21        21.44        37.22        79.17 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 
      112.80        48.89       101.13        15.78        46.68        56.78 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       60.33        84.92        90.12        56.94        52.77        39.55 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
       79.36       102.48        47.97        96.36        89.49        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       97.41        35.90         1.68        12.30        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       11.77        10.36        32.98        21.57        16.67         9.57 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         0.23         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       25.05        24.66        17.19        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91         1.18        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E 
       16.60        14.27         0.53        34.39        14.30        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A54K 
       17.06         1.74         8.42         4.93        17.36        15.42 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       16.27        14.17       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4335 
       53.42        27.78        62.07        80.68        37.25        15.16 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       54.77        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
       12.33        33.99        31.33        72.59        77.98        77.62 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       44.15        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        5.33        61.97        60.59        13.51        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
       11.64        60.95        15.78        48.95        36.53        20.38 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.51         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
       27.22         3.88        46.45        16.47         5.82        43.00 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
       45.07        30.64        41.62        18.51        38.70        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        49.15        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       13.41        24.62        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       26.93        50.01        24.66        39.45        59.44        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       56.35        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       18.87        22.32        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        53.26        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
        7.36        64.57        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
       73.18        66.31        78.18        74.66         1.35       105.93 
TCGA-CW-6093 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
      103.43        18.77        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       69.21        58.75         6.77        14.66        60.59        63.39 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       93.04         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        57.21        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
       12.26        22.78        62.63        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        37.15        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       66.02        18.12         3.91         6.77         7.96        10.29 
TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC TCGA-2K-A9WE 
       70.13         2.01        19.96        15.25        10.85         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JL 
       75.42        34.85        56.81        35.67        38.99        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       30.71        24.33        31.20        29.36        25.58         5.29 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7288 TCGA-A4-7583 
       16.18        22.49         0.13        11.57        61.05         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         0.89         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       29.46        25.64        23.97        23.28        23.31         0.76 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
       19.63        19.73        14.33        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       16.31        15.75         8.28        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
       13.55        30.35        25.08        44.61        49.25         2.20 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
       19.56        21.67        24.56        16.87         3.55        16.77 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        0.46         6.58        33.83        30.58        34.49        12.46 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       10.16        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1.15        43.99        22.06        19.23         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 
       14.86        17.49        12.30        86.76        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        40.83        26.04        30.28        26.04        25.35 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
       13.25        10.88         7.66         0.95        11.97         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
        2.76       123.62        48.26        96.92        93.34        44.84 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       61.28        50.40        49.84        26.27        20.12        11.28 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 
        7.63         7.04         7.17         3.81        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 
        3.02        40.77        80.88        51.19        61.02        54.90 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
       34.19        19.00        24.89         2.40         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
       51.78        48.62        39.25        34.82        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
        6.38        17.98        17.33        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC 
        3.68        27.65         1.05        12.43        17.95         0.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21         4.60        68.12        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25         5.49        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       88.24        67.17        22.26        21.34        16.34        12.36 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       11.97        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
       27.65        20.25         0.36        12.13        25.97        21.44 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.22        42.94         6.61        84.95 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 
       92.58        52.27        16.01        50.60        78.90        12.85 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       11.93        19.00        38.63        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       48.30        43.76        60.03        14.83        21.93         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       38.86        52.11        30.67        25.68        27.39        12.99 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       26.01        29.00        18.64        15.91        18.64        18.05 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       15.62        25.28         6.74         6.02        13.28 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.13              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           129.37            194.79 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            33.04             30.38 
[1] "0.1 - 129.4 (33.0)" "0.1 - 194.8 (30.4)"
[1] "hr=" "1.1"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        41       21        35       14
  XQ LOSS WILD-TYPE     407       82       155       86
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                41               407
  STAGE II               21                82
  STAGE III              35               155
  STAGE IV               14                86
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  XQ LOSS MUTATED    41  22  46   3
  XQ LOSS WILD-TYPE 421 101 205  12
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              41               421
  T2              22               101
  T3              46               205
  T4               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"
                   vv
clus                 N0  N1  N2
  XQ LOSS MUTATED    40  12   2
  XQ LOSS WILD-TYPE 277  31   4
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              40               277
  N1              12                31
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V6, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    69   9
  XQ LOSS WILD-TYPE 473  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     69    9
  XQ LOSS WILD-TYPE  473   80
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              69               473
  1               9                80
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    42  71
  XQ LOSS WILD-TYPE 245 501
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     42   71
  XQ LOSS WILD-TYPE  245  501
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              42               245
  MALE                71               501
[1] 2 2
[1] FALSE
D82V8, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XQ LOSS MUTATED                   38                                46
  XQ LOSS WILD-TYPE                 28                               478
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XQ LOSS MUTATED                                      29
  XQ LOSS WILD-TYPE                                   240
D82V9, multiclass
                                       clus
vv                                      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 38                28
  KIDNEY CLEAR CELL RENAL CARCINOMA                  46               478
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              29               240
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V10, continuous
D82V11, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     5
  XQ LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          17    86
  XQ LOSS WILD-TYPE                        99   616
D82V12, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          5                10
  BLACK OR AFRICAN AMERICAN                     17                99
  WHITE                                         86               616
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D82V13, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  68
  XQ LOSS WILD-TYPE  40 529
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   68
  XQ LOSS WILD-TYPE   40  529
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              68               529
[1] 2 2
[1] FALSE
