[1] "ofn"         "-oTKIPAN-TP"
[1] "opt"       "-OPMUTSIG"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"    "MUTSIG"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIPAN-TP/22506733/KIPAN-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIPAN-TP/22533780/transformed.cor.cli.txt"

nPatients in clinical file=941, in cluster file=882, common to both=882
[1]  82 882
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               31               851 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               31               851 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               68               814 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               68               814 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              120               762 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              120               762 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              127               755 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              127               755 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              103               779 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              103               779 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              161               721 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              161               721 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               47               835 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               47               835 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               836 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               46               836 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              238               644 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              238               644 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              253               629 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              253               629 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22               860 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22               860 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               866 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               866 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              369               513 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              369               513 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              371               511 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              371               511 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               69               813 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               69               813 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              103               779 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              103               779 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               856 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               856 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               858 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               858 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                28                854 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                28                854 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                860 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                860 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                58                824 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                58                824 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                55                827 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                55                827 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               252                630 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               252                630 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               256                626 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               256                626 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                52                830 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                52                830 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                843 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                39                843 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                830 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                52                830 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               281                601 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               281                601 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               268                614 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               268                614 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               196                686 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               196                686 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               222                660 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               222                660 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                828 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                828 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                50                832 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                50                832 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                74                808 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                74                808 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                804 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                78                804 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               233                649 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               233                649 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               237                645 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               237                645 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                72                810 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                72                810 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                64                818 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                64                818 
[1] "XP GAIN MUTATION ANALYSIS"
[1] 3
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              129               753 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              129               753 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              130               752 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              130               752 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              145               737 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              145               737 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              110               772 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              110               772 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               65               817 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               65               817 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               63               819 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               63               819 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              411               471 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              411               471 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              119               763 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              119               763 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               98               784 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               98               784 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               92               790 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               92               790 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               24               858 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               24               858 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               859 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               23               859 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              171               711 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              171               711 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              206               676 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              206               676 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               878 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               878 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               878 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               878 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               721 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               721 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               83               799 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               83               799 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              192               690 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              192               690 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              195               687 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              195               687 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               133                749 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               133                749 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               157                725 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               157                725 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                42                840 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                42                840 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                830 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                830 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 7                875 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 7                875 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                878 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                878 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               137                745 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               137                745 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               265                617 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               265                617 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                68                814 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                68                814 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                18                864 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                18                864 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                854 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                854 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               111                771 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               111                771 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                82                800 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                82                800 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               141                741 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               141                741 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               148                734 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               148                734 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                29                853 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                29                853 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                859 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                859 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                870 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                870 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                876 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                876 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               133                749 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               133                749 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               107                775 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               107                775 
[1] "XP LOSS MUTATION ANALYSIS"
[1] 3
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              114               768 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              114               768 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              113               769 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              113               769 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "KARNOFSKY_PERFORMANCE_SCORE"         
[15] "HISTOLOGICAL_TYPE"                   
[16] "NUMBER_PACK_YEARS_SMOKED"            
[17] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 882 columns.

[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=213,	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=587,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=28,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=10,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=40,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 882 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "KARNOFSKY_PERFORMANCE_SCORE"  
 [9] "HISTOLOGICAL_TYPE"             "NUMBER_PACK_YEARS_SMOKED"     
[11] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
480 127 258  15 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
480 127 258  15 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
480 127 258  15 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
480 127 258  15 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2 
323  44   6 
[1] "table(vv)"
vv
 N0  N1  N2 
323  44   6 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2 
323  44   6 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


 N0  N1  N2 
323  44   6 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=10, binary=FALSE, numeric=TRUE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=44, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=40, 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    11  20
  1P GAIN WILD-TYPE 637 208
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               31               845 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               20               208 
$`1P GAIN MUTATED`
TCGA-AK-3455 TCGA-B0-4815 TCGA-CJ-6027 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-KN-8428 
       22.45        52.21       118.85        12.99        49.25        52.27 
TCGA-A3-3372 TCGA-AK-3430 TCGA-B0-4838 TCGA-B0-5092 TCGA-B0-5109 TCGA-B8-4143 
       24.16        15.78        27.42        15.09        19.30        23.31 
TCGA-B8-5551 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4771 TCGA-BP-4974 TCGA-BP-5175 
        0.53        11.31        12.30         5.33         6.94        30.64 
TCGA-CJ-4873 TCGA-CJ-5679 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-5452 
       74.27        22.32        83.90        18.77        69.21        58.82 
TCGA-MM-A564 TCGA-5P-A9K9 TCGA-BQ-5893 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-7130 
       19.96        19.36         7.92        16.90         3.68        58.19 
TCGA-WN-A9G9 
       26.01 

$`1P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-5088 
      109.91        58.49        28.73        19.73        43.96        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
        0.99        87.12        19.33         2.50        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
      115.00        42.35       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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 
      117.80       122.56       109.41        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       40.70        45.30        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
        7.30        25.32        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       30.48        58.59        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       61.78        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       31.89        33.99        31.33        72.59        77.98         5.98 
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-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 
       61.97        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       25.71        18.87        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-CZ-4853 
       66.31        78.18        74.66         1.35       105.93        25.45 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       47.08        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
      107.41        63.42        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
        2.01        19.43        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-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-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 
       65.13       110.73        51.35        31.73        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.53              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           118.85            194.79 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            22.32             36.53 
[1] "0.5 - 118.8 (22.3)" "0.1 - 194.8 (36.5)"
[1] "hr=" "3.5"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P GAIN MUTATED         7        4        13        6
  1P GAIN WILD-TYPE     447       99       177       98
D1V3, multiclass
           clus
vv          1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                 7               447
  STAGE II                4                99
  STAGE III              13               177
  STAGE IV                6                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
  1P GAIN MUTATED     9   4  18   0
  1P GAIN WILD-TYPE 471 123 240  15
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               9               471
  T2               4               123
  T3              18               240
  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   6   1
  1P GAIN WILD-TYPE 312  38   5
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0              11               312
  N1               6                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 529  83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     17    6
  1P GAIN WILD-TYPE  529   83
   clus
vv  1P GAIN MUTATED 1P GAIN WILD-TYPE
  0              17               529
  1               6                83
[1] 2 2
[1] FALSE
D1V7, binary
                   cls
clus                  0   1
  1P GAIN MUTATED    12  19
  1P GAIN WILD-TYPE 280 571
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     12   19
  1P GAIN WILD-TYPE  280  571
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              12               280
  MALE                19               571
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     9   0
  1P GAIN WILD-TYPE 399   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      9    0
  1P GAIN WILD-TYPE  399    3
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                9               399
  YES               0                 3
[1] 2 2
[1] FALSE
D1V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1P GAIN MUTATED                    1                                22
  1P GAIN WILD-TYPE                 65                               506
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1P GAIN MUTATED                                       8
  1P GAIN WILD-TYPE                                   280
D1V10, multiclass
                                       clus
vv                                      1P GAIN MUTATED 1P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  22               506
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               8               280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, continuous
[1] "Remove cluster labels:" "1P GAIN MUTATED"       
clus
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                2                72 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-2Z-A9JD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ        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-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-MM-A563        TCGA-T7-A92I        TCGA-2Z-A9J3        TCGA-2Z-A9J7 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-2Z-A9J8        TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-A4-A5Y0        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-B9-4114        TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-F9-A97G        TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-G7-A8LB        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        TCGA-UZ-A9PS        TCGA-UZ-A9PX 
"1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" "1P GAIN WILD-TYPE" 
       TCGA-WN-AB4C        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" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P GAIN MUTATED                                  0     1
  1P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED                           2    27
  1P GAIN WILD-TYPE                       119   692
D1V13, multiclass
                                  clus
vv                                 1P GAIN MUTATED 1P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      2               119
  WHITE                                         27               692
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  23
  1P GAIN WILD-TYPE  42 599
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   23
  1P GAIN WILD-TYPE   42  599
                        clus
vv                       1P GAIN MUTATED 1P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO              23               599
[1] 2 2
[1] FALSE

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                 0   1
  1Q GAIN MUTATED    36  32
  1Q GAIN WILD-TYPE 612 196
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               68               808 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               196 
$`1Q GAIN MUTATED`
TCGA-A3-3336 TCGA-A3-3343 TCGA-AK-3450 TCGA-AK-3455 TCGA-B0-4815 TCGA-BP-4331 
       34.29        31.07        58.49        22.45        52.21        80.68 
TCGA-BP-4342 TCGA-CJ-6027 TCGA-CZ-4854 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-A3-3316 
       74.17       118.85        46.16        12.99        49.25        49.08 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 TCGA-B0-4713 TCGA-B0-4838 TCGA-B0-4848 
       24.16        18.87        15.78         6.64        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        52.73        80.91         0.36 
TCGA-B8-4143 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4352 
       23.31         0.53        90.28        61.78        64.27        11.31 
TCGA-BP-4756 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4974 TCGA-BP-5173 TCGA-BP-5175 
       12.30         5.33        68.38         6.94         2.04        30.64 
TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4916 TCGA-CJ-4923 
       46.55       114.41        74.27        66.21        45.14        18.81 
TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CW-5587 TCGA-CW-6090 TCGA-CW-6097 
      129.40        18.87        22.32        73.18        83.90        18.77 
TCGA-CZ-4858 TCGA-CZ-5452 TCGA-G6-A5PC TCGA-MM-A564 TCGA-2Z-A9J2 TCGA-5P-A9K9 
       69.21        58.82         7.96        19.96        59.01        19.36 
TCGA-A4-7287 TCGA-AL-3466 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       19.63         9.63        30.28        25.35         7.66         0.95 
TCGA-BQ-5893 TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-7130 TCGA-IA-A40Y 
        7.92         4.01        16.90         3.68        58.19         2.04 
TCGA-Q2-A5QZ TCGA-WN-A9G9 
       14.07        26.01 

$`1Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3454 
       47.21        38.47        42.97        82.32       109.91        28.73 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       19.73        43.96        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
        8.42        15.42       111.02        94.72        32.61         3.58 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       53.26        75.58       103.43         0.59       107.54         5.46 
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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       99.88       105.60        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       11.90        36.82         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-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-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        7.82         5.98         2.14        57.70         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5094 
       43.30        11.24        11.90         7.30        25.32        10.95 
TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        58.59        66.05        38.63 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        0.53         4.64         5.46         0.23        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60         6.38        48.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       14.17        85.51       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 
       89.36        23.05        77.03        62.24        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       44.94        12.23        31.89        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
       77.98         5.98        41.75        71.80        48.07        13.15 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
       61.68        10.82        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       48.89        49.38        45.50        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       37.48        35.21        28.87         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22        14.17       106.16        54.61        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-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 
       38.56         3.06         4.57       131.08        72.00       133.71 
TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       25.71        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 
       74.66         1.35       105.93        25.45        47.08        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC 
        4.18        10.29        35.87         2.01        19.43        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       11.70         7.04        75.55        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        67.43        18.21         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
       15.75         8.28        12.46        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
       26.04        10.82         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        1.18         0.43        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       23.08        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.36              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.40            194.79 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           24.755            36.675 
[1] "0.4 - 129.4 (24.8)" "0.1 - 194.8 (36.7)"
[1] "hr=" "2.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q GAIN MUTATED        20        8        27       12
  1Q GAIN WILD-TYPE     434       95       163       92
D2V3, multiclass
           clus
vv          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                20               434
  STAGE II                8                95
  STAGE III              27               163
  STAGE IV               12                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
  1Q GAIN MUTATED    23  10  35   0
  1Q GAIN WILD-TYPE 457 117 223  15
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1              23               457
  T2              10               117
  T3              35               223
  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    27   9   2
  1Q GAIN WILD-TYPE 296  35   4
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              27               296
  N1               9                35
  N2               2                 4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    45  11
  1Q GAIN WILD-TYPE 501  78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     45   11
  1Q GAIN WILD-TYPE  501   78
   clus
vv  1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  0              45               501
  1              11                78
[1] 2 2
[1] FALSE
D2V7, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    26  42
  1Q GAIN WILD-TYPE 266 548
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     26   42
  1Q GAIN WILD-TYPE  266  548
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              26               266
  MALE                42               548
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    18   0
  1Q GAIN WILD-TYPE 390   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     18    0
  1Q GAIN WILD-TYPE  390    3
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO               18               390
  YES               0                 3
[1] 2 2
[1] FALSE
D2V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1Q GAIN MUTATED                    0                                50
  1Q GAIN WILD-TYPE                 66                               478
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1Q GAIN MUTATED                                      18
  1Q GAIN WILD-TYPE                                   270
D2V10, multiclass
                                       clus
vv                                      1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  0                66
  KIDNEY CLEAR CELL RENAL CARCINOMA                  50               478
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              18               270
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q GAIN MUTATED                                  0     1
  1Q GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED                           5    61
  1Q GAIN WILD-TYPE                       116   658
D2V13, multiclass
                                  clus
vv                                 1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      5               116
  WHITE                                         61               658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2  49
  1Q GAIN WILD-TYPE  40 573
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   49
  1Q GAIN WILD-TYPE   40  573
                        clus
vv                       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              49               573
[1] 2 2
[1] FALSE

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                 0   1
  2P GAIN MUTATED    88  32
  2P GAIN WILD-TYPE 560 196
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
              120               756 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               32               196 
$`2P GAIN MUTATED`
TCGA-B0-4707 TCGA-BP-4342 TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-5178 TCGA-CZ-4854 
       19.73        74.17        60.59        37.25        62.86        46.16 
TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5561 TCGA-GL-A59T 
       10.16        11.87        11.97        96.92        13.61        17.95 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-KN-8427 TCGA-KO-8410 TCGA-3Z-A93Z TCGA-A3-3372 
       84.89        17.75         0.99       103.10        12.66        24.16 
TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3444 TCGA-B0-4690 
       18.87         0.10       109.41        15.78        48.36         1.41 
TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-5099 TCGA-B0-5109 TCGA-B0-5113 
       57.70        46.59         0.59        15.95        19.30        38.63 
TCGA-B0-5702 TCGA-B4-5832 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5159 
       71.41         5.10         5.46         0.36        25.55        23.74 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 
        6.38        48.53         0.53         4.93       101.06         0.43 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4347 TCGA-BP-4351 
       61.78         0.07        93.99        18.48        44.94        31.89 
TCGA-BP-4756 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4804 TCGA-BP-4969 
       12.30        41.75        13.15        68.38        47.97        58.98 
TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5173 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4644 
       31.30         3.88         2.04        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       109.84        47.67        51.29        49.28 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6032 
      131.08        72.00       133.71       122.83        53.42       119.64 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       73.18        66.31        74.66        69.21        58.75         6.77 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 TCGA-CZ-5984 
       79.63        90.54        94.45        10.85        31.10        67.96 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-2Z-A9J5 TCGA-5P-A9K9 TCGA-A4-A4ZT TCGA-A4-A57E 
       53.46         3.91       100.27        19.36        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
       16.31        15.75         9.63        49.32         2.20        37.51 
TCGA-B9-4117 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 
        0.46         7.92         2.76        51.19         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NI TCGA-IA-A40U 
       51.78        39.25        23.08         3.68        11.84        16.80 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 
        2.04        18.41        29.10        11.41        34.29        42.94 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-V9-A7HT 
       99.12        14.07        28.80        41.62       117.40        31.73 

$`2P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 
      109.91        58.49        28.73        22.45        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 
       12.33        77.62        44.15        11.64        20.38         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 
       41.62        27.62        35.90        48.10        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       31.79        44.55        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 
       21.67        27.68        21.07        21.86        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       13.25        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       14.63         3.02        61.02        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       29.26        19.73        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-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-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      104.55        99.88       105.60        96.62        90.48        92.55 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       11.90        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
       22.65         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      122.56        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       46.78        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4816 
        6.64         3.25        58.45        15.72         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-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       30.48        58.59        66.05        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5844 
       12.00         5.75         1.25         0.53         4.64         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       17.19        50.14        40.04        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       50.14        16.60        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       17.06         1.74        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       90.28        93.34        99.85        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 
       62.07        37.25        21.21        15.62        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       49.08        12.23        11.31        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       77.98         5.98        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-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-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
       36.95        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-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-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       38.30        42.44        37.25        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        19.82         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        74.27        75.06       116.84        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       63.98       115.69        50.01        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.97        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
        3.06         4.57        18.81       129.40        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        25.25        18.15        62.10        73.35        67.00 
TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
       62.66         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 
       85.78        78.18         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       25.45        47.08        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 
       63.42        58.82        79.53        23.74        18.44        91.69 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       55.33        10.22        21.76        69.96        84.30        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-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       14.63        22.78        62.63        12.00        18.12         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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       58.22        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        8.28        12.46        70.19        66.71        62.66        67.73 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        0.95       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       79.86        80.88        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 
       10.68        13.08         2.40         0.43        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       26.01        56.75        73.25        25.22        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       10.55        10.09        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       17.62        31.13        15.48        99.78        87.09         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        27.06        11.93        19.00        16.31 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       26.47        53.10        43.76        18.02        26.20       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C 
       47.47        65.13       110.73        51.35        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.07              0.10 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           133.71            194.79 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            31.20             36.44 
[1] "0.1 - 133.7 (31.2)" "0.1 - 194.8 (36.4)"
[1] "hr=" "1.2"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P GAIN MUTATED        56       13        31       18
  2P GAIN WILD-TYPE     398       90       159       86
D3V3, multiclass
           clus
vv          2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                56               398
  STAGE II               13                90
  STAGE III              31               159
  STAGE IV               18                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
  2P GAIN MUTATED    57  16  43   4
  2P GAIN WILD-TYPE 423 111 215  11
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1              57               423
  T2              16               111
  T3              43               215
  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    43  11   2
  2P GAIN WILD-TYPE 280  33   4
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              43               280
  N1              11                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"
D3V6, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    75  14
  2P GAIN WILD-TYPE 471  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     75   14
  2P GAIN WILD-TYPE  471   75
   clus
vv  2P GAIN MUTATED 2P GAIN WILD-TYPE
  0              75               471
  1              14                75
[1] 2 2
[1] FALSE
D3V7, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    40  80
  2P GAIN WILD-TYPE 252 510
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     40   80
  2P GAIN WILD-TYPE  252  510
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              40               252
  MALE                80               510
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    48   1
  2P GAIN WILD-TYPE 360   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     48    1
  2P GAIN WILD-TYPE  360    2
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO               48               360
  YES               1                 2
[1] 2 2
[1] FALSE
D3V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2P GAIN MUTATED                    2                                76
  2P GAIN WILD-TYPE                 64                               452
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2P GAIN MUTATED                                      42
  2P GAIN WILD-TYPE                                   246
D3V10, multiclass
                                       clus
vv                                      2P GAIN MUTATED 2P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  2                64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  76               452
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              42               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"
D3V11, continuous
D3V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P GAIN MUTATED                                  0     2
  2P GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED                          13   102
  2P GAIN WILD-TYPE                       108   617
D3V13, multiclass
                                  clus
vv                                 2P GAIN MUTATED 2P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                14
  BLACK OR AFRICAN AMERICAN                     13               108
  WHITE                                        102               617
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V14, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     6  82
  2P GAIN WILD-TYPE  36 540
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      6   82
  2P GAIN WILD-TYPE   36  540
                        clus
vv                       2P GAIN MUTATED 2P GAIN WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              82               540
[1] 2 2
[1] FALSE

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                 0   1
  2Q GAIN MUTATED    94  33
  2Q GAIN WILD-TYPE 554 195
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
              127               749 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               33               195 
$`2Q GAIN MUTATED`
TCGA-AK-3450 TCGA-B0-4707 TCGA-BP-4342 TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-5178 
       58.49        19.73        74.17        60.59        37.25        62.86 
TCGA-CZ-4854 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-7046 
       46.16        21.07        10.16        11.87        11.97        96.92 
TCGA-DW-5561 TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-KN-8427 TCGA-KO-8410 
       13.61        17.95        84.89        17.75         0.99       103.10 
TCGA-3Z-A93Z TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3444 
       12.66        24.16        18.87         0.10       109.41        48.36 
TCGA-B0-4690 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-5099 TCGA-B0-5109 
        1.41        57.70        46.59         0.59        15.95        19.30 
TCGA-B0-5113 TCGA-B0-5702 TCGA-B4-5832 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4620 
       38.63        71.41         5.10         5.46         0.36        25.55 
TCGA-B8-5159 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 
       23.74         6.38        48.53         0.53         4.93       101.06 
TCGA-BP-4166 TCGA-BP-4170 TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
        0.43        77.03        61.78         0.07        93.99        18.48 
TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 
       44.94        31.89        12.30        41.75        13.15        68.38 
TCGA-BP-4804 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-5001 TCGA-BP-5173 
       47.97        58.98        31.30         3.88        38.70         2.04 
TCGA-BP-5174 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4644 TCGA-CJ-4876 TCGA-CJ-4893 
       74.20        37.22        34.95        11.05        64.27        24.66 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 
      109.84        47.67        51.29        49.28       131.08        72.00 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5588 
      133.71       122.83        53.42       119.64        73.18        66.31 
TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-5456 TCGA-CZ-5457 
       74.66        69.21        58.75         6.77        79.63        90.54 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5469 TCGA-DV-A4VX TCGA-EU-5905 TCGA-2Z-A9J5 
       94.45        10.85        31.10        53.46         3.91       100.27 
TCGA-2Z-A9JR TCGA-5P-A9K9 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
        5.29        19.36        16.96         8.48        16.31        15.75 
TCGA-AL-3466 TCGA-AL-3471 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B9-4117 
        9.63        49.32        67.73         2.20        37.51         0.46 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-DZ-6133 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
        7.92         2.76        51.19         1.18         4.01        51.78 
TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NI TCGA-IA-A40U 
       39.25        25.84        23.08         3.68        11.84        16.80 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5E8 
        2.04        18.41        29.10        11.41        34.29        42.94 
TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UZ-A9PK TCGA-UZ-A9PQ 
       99.12        14.07        28.80        41.62       117.40        86.27 
TCGA-V9-A7HT 
       31.73 

$`2Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
      109.91        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 
       94.72        32.61         3.58        80.68        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 
       77.62        44.15        11.64        20.38         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       27.62        35.90        48.10        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 
       27.68        21.86        19.23        26.04        13.25        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
       26.27        20.12        11.28        48.85       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       61.02        67.17        16.34        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-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-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 
      100.47       103.40        92.71        16.67       104.55        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 
      105.60        96.62        90.48        92.55        11.90        36.82 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
       11.18        10.62        29.10       117.80       122.56        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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-B0-4713 
        3.62        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
        3.25        58.45        15.72         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-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       58.59        66.05        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
      129.67        85.78        86.47       126.28        80.91        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 
        5.75         1.25         0.53         4.64         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        40.04        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       16.60        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 
       93.34        99.85        89.36        23.05        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4349 
       21.21        15.62        52.24        62.86        49.08        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       11.31        33.99        31.33        72.59        77.98         5.98 
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-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4991 
       14.93        36.07        33.34        46.45        36.95        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5007 
       16.47        43.00        30.64        18.51        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5176 
       35.21        28.87         6.35        79.30        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        9.63        74.40        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16       114.41        54.61        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 
       30.64        51.52        63.98       115.69        50.01        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       50.24        56.35        49.97        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       129.40 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       25.71        18.87        22.32        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       73.35        67.00        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4863 
       83.90        18.77        25.45        47.08        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       18.44        91.69        55.33        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        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-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01        58.22        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       24.33        31.20        29.36         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
       14.33        12.46         8.28        12.46        70.19        66.71 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       62.66        41.13        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.66         0.95       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        79.86        80.88        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 
       24.89        10.68        13.08         2.40         0.43        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        71.44        25.15        20.52        25.25        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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       26.01        56.75        73.25        25.22        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       10.55        10.09        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA 
       17.62        31.13        15.48        99.78        87.09         6.61 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        27.06        11.93        19.00        16.31 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       26.47        53.10        43.76        18.02        26.20       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       65.13       110.73        51.35        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.07              0.10 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           133.71            194.79 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            31.73             36.36 
[1] "0.1 - 133.7 (31.7)" "0.1 - 194.8 (36.4)"
[1] "hr=" "1.1"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q GAIN MUTATED        62       13        31       19
  2Q GAIN WILD-TYPE     392       90       159       85
D4V3, multiclass
           clus
vv          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                62               392
  STAGE II               13                90
  STAGE III              31               159
  STAGE IV               19                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
  2Q GAIN MUTATED    63  17  43   4
  2Q GAIN WILD-TYPE 417 110 215  11
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1              63               417
  T2              17               110
  T3              43               215
  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    45  11   3
  2Q GAIN WILD-TYPE 278  33   3
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              45               278
  N1              11                33
  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"
D4V6, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    79  14
  2Q GAIN WILD-TYPE 467  75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     79   14
  2Q GAIN WILD-TYPE  467   75
   clus
vv  2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  0              79               467
  1              14                75
[1] 2 2
[1] FALSE
D4V7, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    45  82
  2Q GAIN WILD-TYPE 247 508
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     45   82
  2Q GAIN WILD-TYPE  247  508
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              45               247
  MALE                82               508
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    53   1
  2Q GAIN WILD-TYPE 355   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     53    1
  2Q GAIN WILD-TYPE  355    2
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO               53               355
  YES               1                 2
[1] 2 2
[1] FALSE
D4V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2Q GAIN MUTATED                    2                                78
  2Q GAIN WILD-TYPE                 64                               450
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2Q GAIN MUTATED                                      47
  2Q GAIN WILD-TYPE                                   241
D4V10, multiclass
                                       clus
vv                                      2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  2                64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  78               450
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              47               241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q GAIN MUTATED                                  0     2
  2Q GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED                          14   108
  2Q GAIN WILD-TYPE                       107   611
D4V13, multiclass
                                  clus
vv                                 2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                14
  BLACK OR AFRICAN AMERICAN                     14               107
  WHITE                                        108               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"
D4V14, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     7  88
  2Q GAIN WILD-TYPE  35 534
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7   88
  2Q GAIN WILD-TYPE   35  534
                        clus
vv                       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO              88               534
[1] 2 2
[1] FALSE

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                 0   1
  3P GAIN MUTATED    77  23
  3P GAIN WILD-TYPE 571 205
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
              100               776 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23               205 
$`3P GAIN MUTATED`
TCGA-KL-8339 TCGA-B0-4712 TCGA-AL-3468 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       28.11        43.96        76.64        21.07        10.16        21.86 
TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       26.04        96.92        48.85        35.93        37.55        24.46 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-KL-8331 
       17.95        84.89        17.75        21.60        15.91        98.96 
TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 
       24.79        62.37        49.97         0.99        52.27        42.35 
TCGA-A3-3374 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-5081 TCGA-B0-5084 
       43.20        94.19        83.21         3.62        11.90         7.30 
TCGA-B4-5835 TCGA-BP-4337 TCGA-BP-4352 TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5175 
        0.53         0.07        11.31        58.98        43.00        30.64 
TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4897 TCGA-CW-6087 TCGA-CZ-4861 TCGA-CZ-5469 
       19.82        14.17       109.84         1.35        14.66        31.10 
TCGA-2K-A9WE TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9KA 
        7.04       100.27        56.91        49.58        78.64        12.99 
TCGA-A4-7287 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
       19.63        23.97         0.76        19.73        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-4103 
       16.96        16.31        49.32         2.20        37.51        30.58 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH 
       28.18         0.46         1.15        43.99        22.06        17.49 
TCGA-BQ-5881 TCGA-BQ-7045 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 
       47.80        48.26         7.04         3.81        40.77        51.19 
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-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S 
       11.21        81.93        58.19        11.84        25.22        85.78 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVM 
       18.41        29.10        11.41        87.09         6.61        50.60 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK 
       28.80        19.00        16.31        41.62        53.10       117.40 
TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       71.24        47.47        51.35        31.73 

$`3P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        19.73        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B9-A44B 
        0.89        12.99        49.25        21.67        27.68        11.87 
TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       19.23        13.25        11.97        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       11.28        13.61       129.86        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
        3.02        61.02        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ 
       19.73        41.33        62.83        86.37        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-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-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.56        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       54.74       151.96        44.91       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-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
      104.52         3.55        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       59.08       115.00       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80       122.56       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61       109.51        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        37.58        38.40        82.45        72.89        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-B0-4700 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        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5092 
       70.52        20.94        43.30        11.24        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 
       16.67        12.00         5.75         5.10         1.25         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       61.78        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        21.21        15.62        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       24.62        33.47        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
      115.69        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18        74.66       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4864 
       47.08        69.21        58.75         6.77        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J1 
        2.01        19.43        19.96        16.37        11.70        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       59.01        58.22         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
        5.29         0.13        12.82        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       22.26        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        67.43        18.21         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-A57E TCGA-A4-A5XZ 
       25.64        23.28        23.31        19.63         8.48        15.75 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46         9.63        70.19        66.71        62.66 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       67.73        41.13        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 
       33.83        29.03        34.49        12.46        50.50        26.40 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.61        17.23         0.16        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92         2.76       123.62        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 
       50.40        49.84         7.63         7.17        79.86        80.88 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY 
       74.60        34.19        19.00        24.89        10.68         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43         4.01        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        20.52        25.84        25.25        23.08        80.65 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
       16.31        26.01        56.75        73.25        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
        2.04        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       12.76        10.55        10.09        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVO 
       42.94        99.12        92.58        52.27        16.01        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
       14.07        47.90        49.45        44.61        27.06        11.93 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM 
       26.47        43.76        18.02        26.20       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       37.35        98.96        86.27        30.67        65.13       110.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.07              0.10 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           194.79            153.73 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           27.075            36.835 
[1] "0.1 - 194.8 (27.1)" "0.1 - 153.7 (36.8)"
[1] "hr=" "1.1"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P GAIN MUTATED        57       16        11       11
  3P GAIN WILD-TYPE     397       87       179       93
D5V3, multiclass
           clus
vv          3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                57               397
  STAGE II               16                87
  STAGE III              11               179
  STAGE IV               11                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
  3P GAIN MUTATED    61  20  18   3
  3P GAIN WILD-TYPE 419 107 240  12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1              61               419
  T2              20               107
  T3              18               240
  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    20   8   1
  3P GAIN WILD-TYPE 303  36   5
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              20               303
  N1               8                36
  N2               1                 5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    42   7
  3P GAIN WILD-TYPE 504  82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     42    7
  3P GAIN WILD-TYPE  504   82
   clus
vv  3P GAIN MUTATED 3P GAIN WILD-TYPE
  0              42               504
  1               7                82
[1] 2 2
[1] FALSE
D5V7, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    27  76
  3P GAIN WILD-TYPE 265 514
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     27   76
  3P GAIN WILD-TYPE  265  514
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              27               265
  MALE                76               514
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    66   0
  3P GAIN WILD-TYPE 342   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     66    0
  3P GAIN WILD-TYPE  342    3
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO               66               342
  YES               0                 3
[1] 2 2
[1] FALSE
D5V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3P GAIN MUTATED                    9                                19
  3P GAIN WILD-TYPE                 57                               509
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3P GAIN MUTATED                                      75
  3P GAIN WILD-TYPE                                   213
D5V10, multiclass
                                       clus
vv                                      3P GAIN MUTATED 3P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  19               509
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              75               213
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P GAIN MUTATED                                  1     2
  3P GAIN WILD-TYPE                                1    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED                          14    80
  3P GAIN WILD-TYPE                       107   639
D5V13, multiclass
                                  clus
vv                                 3P GAIN MUTATED 3P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               1                 1
  ASIAN                                          2                14
  BLACK OR AFRICAN AMERICAN                     14               107
  WHITE                                         80               639
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     4  79
  3P GAIN WILD-TYPE  38 543
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      4   79
  3P GAIN WILD-TYPE   38  543
                        clus
vv                       3P GAIN MUTATED 3P GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                38
  NOT HISPANIC OR LATINO              79               543
[1] 2 2
[1] FALSE

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                 0   1
  3Q GAIN MUTATED   113  45
  3Q GAIN WILD-TYPE 535 183
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
              158               718 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               45               183 
$`3Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-B0-4712 TCGA-B8-4621 TCGA-BP-4762 TCGA-AL-3468 
       28.11        38.47        43.96        25.91        44.15        76.64 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-7046 
       21.07        10.16        21.86        11.87        26.04        96.92 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       35.93        37.55        24.46        17.95        84.89        67.17 
TCGA-PJ-A5Z9 TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 
       17.75        21.60        15.91        98.96        24.79        62.37 
TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 TCGA-A3-3374 TCGA-AK-3434 
       49.97         0.99        52.27        42.35        43.20        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-4699 TCGA-B0-4713 
      109.51        94.19        83.21         1.41         3.62         6.64 
TCGA-B0-4833 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5097 TCGA-B0-5102 TCGA-B0-5109 
       78.44        11.90         7.30        21.86        90.87        19.30 
TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5710 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 
       41.88        85.78        79.89         0.53         5.46        23.31 
TCGA-B8-4620 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4167 TCGA-BP-4337 TCGA-BP-4338 
       25.55         6.38         0.53        89.36         0.07        93.99 
TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4960 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4994 
       11.31         5.98        71.41        58.98        31.30        43.00 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4871 
        6.35        30.64        19.82        14.17       114.41        79.66 
TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-6028 TCGA-CJ-6033 TCGA-CW-5591 
      109.84        56.35        47.67        53.42         7.36        74.66 
TCGA-CW-6087 TCGA-CW-6097 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5460 
        1.35        18.77        69.21         6.77        14.66        94.45 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-DV-A4VX TCGA-2K-A9WE TCGA-2Z-A9J2 
       69.96        84.30        31.10        53.46         7.04        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY TCGA-5P-A9K2 TCGA-5P-A9K4 
       58.22       100.27        56.91        49.58        78.64        71.80 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 
       12.99        12.39        19.63        30.48        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5DU 
        0.76        19.73        14.33        12.46        16.96        16.31 
TCGA-A4-A5XZ TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-4103 TCGA-B9-4114 
       15.75        49.32         2.20        37.51        30.58        28.18 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 
        0.46         1.15        43.99        22.06        17.49        47.80 
TCGA-BQ-5890 TCGA-BQ-7045 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
        7.66        48.26         7.04         3.81        40.77        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 
       51.19        74.60        34.19        13.08         2.40        51.78 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 
       17.98        16.90       194.79        11.21        81.93        58.19 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A83S TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        25.22        85.78        18.41        29.10        11.41 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-P4-AAVM TCGA-Q2-A5QZ 
       99.78        87.09         6.61        16.01        50.60        14.07 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PK 
       28.80        19.00        16.31        41.62        53.10       117.40 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 
      125.29        37.35        71.24        30.67        47.47       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       51.35        31.73 

$`3Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       34.29        31.07        42.97        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
       28.73        22.45        19.73        52.21        18.51       112.80 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      133.94        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
        3.58        80.68        74.17        54.77        12.33        77.62 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       31.79        44.55        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       67.17        61.05        21.37         0.89        12.99        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 
       21.67        27.68        19.23        13.25        11.97        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IZ-A6M8 
       13.78         3.75        14.63         3.02        61.02        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       12.13        29.26        19.73        41.33        62.83        86.37 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48       108.62        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 
       92.55        30.25        44.84        86.56        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 
       71.41        28.80        54.74       151.96        44.91       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 
       25.91        65.19       104.52         3.55        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 
        2.50        11.21        59.08       115.00       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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-3430 
       10.62        29.10       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       73.68       112.08        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       40.70         1.41         3.32         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-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        2.14        57.70         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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-B0-4834 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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       11.24        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       52.08        15.95        62.89        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       58.59        66.05        38.63        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
      129.67        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      149.16       105.37       130.65       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        5.10         1.25         4.64         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
       49.97        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       16.60        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       15.62        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        31.89        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       77.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        46.45        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       28.87        79.30         2.04        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 
       34.95         0.95       115.00        46.55        73.22       106.16 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       50.24        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       67.00        62.66       119.64        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 
        5.39        85.78        73.18        66.31        78.18       105.93 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 
       83.90        25.45        47.08        58.75        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        90.54        91.69        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       21.76        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-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        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-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
       11.70        75.55         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
        5.29         0.13        12.82        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KE 
       22.26        15.48        62.93        43.04        19.36        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        18.21         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8517 
        0.23        16.64        29.46        25.64        23.28        19.63 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
        8.48         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       62.66        67.73        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        29.03        34.49        12.46        50.50 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI 
       26.40        20.61        17.23         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-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92         2.76       123.62        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 
       50.40        49.84         7.63         7.17        79.86        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       24.89        10.68         1.18         0.43         4.01        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       25.25        23.08        80.65        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ 
        1.05        12.43        12.89        16.31        26.01        56.75 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V 
       73.25        16.80        19.99         2.04        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       31.13        15.48        42.94        99.12        92.58        52.27 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
       78.90        47.90        49.45        44.61        27.06        11.93 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PP 
       26.47        43.76        18.02        26.20       103.63        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PX TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       86.27        65.13        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.07              0.10 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           194.79            153.73 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
           30.655            36.510 
[1] "0.1 - 194.8 (30.7)" "0.1 - 153.7 (36.5)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q GAIN MUTATED        76       21        30       24
  3Q GAIN WILD-TYPE     378       82       160       80
D6V3, multiclass
           clus
vv          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                76               378
  STAGE II               21                82
  STAGE III              30               160
  STAGE IV               24                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    83  26  45   6
  3Q GAIN WILD-TYPE 397 101 213   9
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1              83               397
  T2              26               101
  T3              45               213
  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
  3Q GAIN MUTATED    44  13   1
  3Q GAIN WILD-TYPE 279  31   5
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              44               279
  N1              13                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  18
  3Q GAIN WILD-TYPE 474  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     72   18
  3Q GAIN WILD-TYPE  474   71
   clus
vv  3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  0              72               474
  1              18                71
[1] 2 2
[1] FALSE
D6V7, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    41 120
  3Q GAIN WILD-TYPE 251 470
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     41  120
  3Q GAIN WILD-TYPE  251  470
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              41               251
  MALE               120               470
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    92   0
  3Q GAIN WILD-TYPE 316   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     92    0
  3Q GAIN WILD-TYPE  316    3
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO               92               316
  YES               0                 3
[1] 2 2
[1] FALSE
D6V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3Q GAIN MUTATED                    9                                58
  3Q GAIN WILD-TYPE                 57                               470
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3Q GAIN MUTATED                                      94
  3Q GAIN WILD-TYPE                                   194
D6V10, multiclass
                                       clus
vv                                      3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  58               470
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              94               194
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q GAIN MUTATED                                  2     2
  3Q GAIN WILD-TYPE                                0    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED                          20   128
  3Q GAIN WILD-TYPE                       101   591
D6V13, multiclass
                                  clus
vv                                 3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          2                14
  BLACK OR AFRICAN AMERICAN                     20               101
  WHITE                                        128               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"
D6V14, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     7 120
  3Q GAIN WILD-TYPE  35 502
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      7  120
  3Q GAIN WILD-TYPE   35  502
                        clus
vv                       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO             120               502
[1] 2 2
[1] FALSE

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  4P GAIN MUTATED    35  11
  4P GAIN WILD-TYPE 613 217
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               46               830 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               11               217 
$`4P GAIN MUTATED`
TCGA-KL-8339 TCGA-BP-4342 TCGA-BQ-5892 TCGA-UZ-A9PO TCGA-KL-8324 TCGA-KL-8327 
       28.11        74.17        11.97        62.83       153.73       137.06 
TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
       98.96        24.79        62.37       151.96        49.97        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 
       25.48        25.91       104.52         3.55         2.50        11.21 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       42.35        10.68       100.47       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 
      105.60        96.62        43.20        15.78       112.08        94.19 
TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4813 TCGA-BP-4166 TCGA-BP-4352 TCGA-BP-4977 
        3.32        28.47         0.59         0.43        11.31        14.93 
TCGA-BP-4989 TCGA-BP-4994 TCGA-AL-3466 TCGA-B9-4114 TCGA-B9-A5W9 TCGA-G7-6789 
        3.88        43.00         9.63        28.18         0.16         4.01 
TCGA-G7-6795 TCGA-G7-A8LC TCGA-SX-A7SR TCGA-WN-AB4C 
       39.25        23.08        26.47        39.06 

$`4P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        41.33        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
        6.74        38.07        23.84       109.22        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-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       44.91       123.12        51.06        31.33       129.37        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8434 
       65.19         0.99        52.27        87.12        19.33        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      115.00       100.87       105.47       103.40        92.71        16.67 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
      109.41        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       82.45        72.89        12.13        40.70         1.41         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-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72        46.59         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-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
       85.51        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        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-4343 
       15.62         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-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-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-4981 TCGA-BP-4982 TCGA-BP-4983 
       45.50         6.94        47.11        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       31.30        36.95        46.45        16.47        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39        93.04       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       11.05        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        41.62        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.16              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           153.73            194.79 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           28.325            35.915 
[1] "0.2 - 153.7 (28.3)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1.2"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P GAIN MUTATED        18       13         7        8
  4P GAIN WILD-TYPE     436       90       183       96
D7V3, multiclass
           clus
vv          4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                18               436
  STAGE II               13                90
  STAGE III               7               183
  STAGE IV                8                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
  4P GAIN MUTATED    18  14  13   2
  4P GAIN WILD-TYPE 462 113 245  13
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1              18               462
  T2              14               113
  T3              13               245
  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 297  41   4
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0              26               297
  N1               3                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"
D7V6, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    24   5
  4P GAIN WILD-TYPE 522  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     24    5
  4P GAIN WILD-TYPE  522   84
   clus
vv  4P GAIN MUTATED 4P GAIN WILD-TYPE
  0              24               522
  1               5                84
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    15  32
  4P GAIN WILD-TYPE 277 558
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     15   32
  4P GAIN WILD-TYPE  277  558
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              15               277
  MALE                32               558
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED    31   0
  4P GAIN WILD-TYPE 377   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     31    0
  4P GAIN WILD-TYPE  377    3
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO               31               377
  YES               0                 3
[1] 2 2
[1] FALSE
D7V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4P GAIN MUTATED                   24                                13
  4P GAIN WILD-TYPE                 42                               515
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4P GAIN MUTATED                                      10
  4P GAIN WILD-TYPE                                   278
D7V10, multiclass
                                       clus
vv                                      4P GAIN MUTATED 4P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                  13               515
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              10               278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P GAIN MUTATED                                  0     1
  4P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED                           3    43
  4P GAIN WILD-TYPE                       118   676
D7V13, multiclass
                                  clus
vv                                 4P GAIN MUTATED 4P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      3               118
  WHITE                                         43               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"
D7V14, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     3  30
  4P GAIN WILD-TYPE  39 592
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      3   30
  4P GAIN WILD-TYPE   39  592
                        clus
vv                       4P GAIN MUTATED 4P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              30               592
[1] 2 2
[1] FALSE

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED    36   9
  4Q GAIN WILD-TYPE 612 219
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               45               831 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                9               219 
$`4Q GAIN MUTATED`
TCGA-KL-8339 TCGA-BP-4342 TCGA-BQ-5892 TCGA-UZ-A9PO TCGA-KL-8324 TCGA-KL-8327 
       28.11        74.17        11.97        62.83       153.73       137.06 
TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
       98.96        24.79        62.37       151.96        49.97        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 
       25.48        25.91       104.52         3.55         2.50        11.21 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       42.35        10.68       100.47       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 
      105.60        96.62        43.20        15.78       112.08        94.19 
TCGA-B0-4696 TCGA-B0-4813 TCGA-BP-4166 TCGA-BP-4352 TCGA-BP-4977 TCGA-BP-4989 
       28.47         0.59         0.43        11.31        14.93         3.88 
TCGA-BP-4994 TCGA-BP-5177 TCGA-B9-4114 TCGA-B9-A5W9 TCGA-G7-6789 TCGA-G7-6795 
       43.00         9.63        28.18         0.16         4.01        39.25 
TCGA-G7-A8LC TCGA-SX-A7SR TCGA-WN-AB4C 
       23.08        26.47        39.06 

$`4Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        41.33        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
        6.74        38.07        23.84       109.22        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-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       44.91       123.12        51.06        31.33       129.37        87.91 
TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8434 
       65.19         0.99        52.27        87.12        19.33        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      115.00       100.87       105.47       103.40        92.71        16.67 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
      109.41        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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-B0-4710 
        3.62        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 
        6.64         3.25        58.45        15.72        46.59         5.52 
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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       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-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       62.86        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4787 
       61.97        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50         6.94        47.11        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 
       46.45        31.30        36.95        46.45        16.47        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39        93.04       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       34.49        12.46        50.50        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
        1.15        43.99        22.06        17.23        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       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 
       90.90        11.05        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       19.00        16.31        41.62        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       51.35        31.73        26.01        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             0.16              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           153.73            194.79 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            28.47             35.90 
[1] "0.2 - 153.7 (28.5)" "0.1 - 194.8 (35.9)"
[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     435       90       183       98
D8V3, multiclass
           clus
vv          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                19               435
  STAGE II               13                90
  STAGE III               7               183
  STAGE IV                6                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
  4Q GAIN MUTATED    19  14  12   1
  4Q GAIN WILD-TYPE 461 113 246  14
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1              19               461
  T2              14               113
  T3              12               246
  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 298  42   4
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0              25               298
  N1               2                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"
D8V6, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    25   3
  4Q GAIN WILD-TYPE 521  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     25    3
  4Q GAIN WILD-TYPE  521   86
   clus
vv  4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  0              25               521
  1               3                86
[1] 2 2
[1] FALSE
D8V7, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    16  30
  4Q GAIN WILD-TYPE 276 560
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     16   30
  4Q GAIN WILD-TYPE  276  560
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              16               276
  MALE                30               560
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED    31   0
  4Q GAIN WILD-TYPE 377   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     31    0
  4Q GAIN WILD-TYPE  377    3
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO               31               377
  YES               0                 3
[1] 2 2
[1] FALSE
D8V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4Q GAIN MUTATED                   24                                13
  4Q GAIN WILD-TYPE                 42                               515
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4Q GAIN MUTATED                                       9
  4Q GAIN WILD-TYPE                                   279
D8V10, multiclass
                                       clus
vv                                      4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                  13               515
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               9               279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
D8V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q GAIN MUTATED                                  0     1
  4Q GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED                           3    42
  4Q GAIN WILD-TYPE                       118   677
D8V13, multiclass
                                  clus
vv                                 4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      3               118
  WHITE                                         42               677
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     3  28
  4Q GAIN WILD-TYPE  39 594
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      3   28
  4Q GAIN WILD-TYPE   39  594
                        clus
vv                       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              28               594
[1] 2 2
[1] FALSE

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED   168  69
  5P GAIN WILD-TYPE 480 159
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
              237               639 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               69               159 
$`5P GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-B0-4707 TCGA-B0-4712 
       28.11        38.47        34.29        42.97        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5694 TCGA-B2-5635 TCGA-BP-4158 TCGA-BP-4160 
       52.21        18.51        15.78        24.82       111.02        94.72 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4799 TCGA-BP-4965 TCGA-BP-4976 
       74.17        54.77        12.33        37.25        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4999 TCGA-BP-5168 TCGA-BP-5191 TCGA-BP-5201 
       25.81        27.22        41.62        48.10        31.79        31.27 
TCGA-CJ-4636 TCGA-CJ-4904 TCGA-CJ-6027 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       63.25       108.56       118.85        11.67        37.15        66.28 
TCGA-BQ-5892 TCGA-DW-7838 TCGA-KL-8327 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       11.97        24.46       137.06         3.55         0.99        52.27 
TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3316 TCGA-A3-3322 
       42.35        10.68       105.60        12.66        49.08        48.59 
TCGA-A3-3324 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3374 
       38.99        48.82        52.93        88.37        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-A6NL TCGA-A3-A6NN TCGA-AK-3429 TCGA-AK-3430 
       18.87        65.52        22.65         0.10       109.41        15.78 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 TCGA-AK-3460 TCGA-AK-3461 
      109.51        94.19        78.64        83.21        82.45        72.89 
TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4710 
       28.47         1.38         3.62        65.10         5.98        57.70 
TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        6.64        46.59         5.52         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-B0-5094 TCGA-B0-5095 
       29.03         2.27        20.94        43.30        10.95         8.05 
TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5121 
       90.87        52.54        19.30        38.63        52.73        48.82 
TCGA-B0-5400 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 
       56.98        85.78        86.47        80.91        71.41       149.16 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 TCGA-B4-5838 TCGA-B8-4620 
       89.49        91.46        35.90        31.30         5.46        25.55 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54I 
       23.74        27.02         6.38        48.53         0.53         4.93 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4337 
      101.06         0.43        61.78        64.27        54.90         0.07 
TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4758 
       93.99        62.86        44.94        31.89        11.31        72.59 
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-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       47.97        63.62        58.68        61.22         6.74        57.40 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4991 
       58.98        48.89        46.45        31.30         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5173 
       16.47        43.00        37.02        37.48        79.30         2.04 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5200 TCGA-BP-5202 
       30.64         9.63        37.22        13.35        34.95         0.95 
TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 
       46.55       106.16        11.05        83.97        79.66        74.27 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 
      116.84        66.21       113.46        30.64       115.69        50.01 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 
      109.84        50.24        56.35        49.97        51.29        49.28 
TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 
       54.48       131.08       133.71        22.32       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
       73.35        67.00        53.42        85.78        73.18        66.31 
TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       74.66        25.45        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       58.82        79.63        90.54        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 
       69.96        22.52         2.40         1.94        12.69        67.96 
TCGA-CZ-5986 TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 
       12.26         3.91         4.18        10.29         2.01        19.96 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-2Z-A9J3 TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7287 
       16.37         7.04        58.22        12.82        19.36        19.63 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 
       30.48        29.46         0.76        12.46         8.48         9.63 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 
       62.66        41.13        20.32         0.46         0.16        25.35 
TCGA-BQ-5891 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC 
        0.95        79.86        19.00        13.08         4.01        23.08 
TCGA-GL-A4EM TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5EB 
        1.05        58.19        73.25         2.04        18.41        99.12 
TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SQ 
       16.01        14.07        41.62 

$`5P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       31.07        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B8-4621 
      112.80       133.94        70.68       119.38       126.05        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
        1.18         8.42        15.42        32.61         3.58        80.68 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 
       77.62        44.15        60.59        11.64        20.38         6.94 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5181 
        5.82        45.07        27.62        35.90        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-5689 
       27.02        44.55       105.37        26.93        27.65        53.26 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5575 TCGA-DV-5576 
       43.69        45.96        65.88        12.16        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        13.25        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       37.55        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      109.22        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 
      104.52        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       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 
       16.67       104.55       103.10        99.88        96.62        90.48 
TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       92.55        11.90        36.82         0.53        39.16        24.16 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3335 
       49.02        37.15        49.58        36.36        37.38        62.01 
TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3363 
        4.50        45.53        29.92        18.44        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-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A8CQ 
       18.64        28.31        20.28        33.47        15.39         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 
       11.18        10.62        29.10       117.80       122.56        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 
      112.08        68.61        46.78        48.36        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        12.13        40.70         1.41         3.32 
TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4701 
        1.41         4.57         2.53         3.48        19.00         7.82 
TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 
        2.14         3.25        58.45        15.72         0.59        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 
       33.50        16.77        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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       26.07        36.85        70.52        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       25.32        15.09         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5116 
       62.89        90.48        30.48        58.59        66.05        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 
       52.87        51.02        38.43        46.39        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
      129.67       126.28        73.84       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
      131.15        32.61         1.68        31.96        21.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       50.14        40.04         0.85        24.23        50.14        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-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 
       17.36        16.27        14.17        85.51        90.28        93.34 
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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       18.48        52.24        49.08        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       12.30        77.98        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        5.33        61.97        13.51        56.91        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 
       36.53        10.98        36.95         6.71        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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4998 TCGA-BP-5000 
       14.93        36.07        33.34        36.95        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5176 
       38.70        35.21        28.87         6.35        74.20        52.27 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 
       74.40        38.30        42.44        37.25        22.78        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4634 
       23.47        13.41        24.62        33.47        19.82       115.00 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       73.22        14.17       114.41        54.61        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-4893 TCGA-CJ-4895 
       57.83        64.18        51.52        63.98        24.66        39.45 
TCGA-CJ-4901 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       47.67        49.18        50.33        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57        18.81        72.00       129.40        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       25.25        18.15        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 
       92.02        81.83         5.39        78.18         1.35       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       83.90        18.77        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 
       14.66        79.53        23.74        18.44        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5987 
       94.45        84.30        31.10        80.19        65.65        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       22.78        62.63        53.46        12.00        18.12         6.77 
TCGA-G6-A5PC TCGA-G6-A8L8 TCGA-MM-A563 TCGA-T7-A92I TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        7.96        35.87        19.43        11.70        75.55        59.01 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 
       35.18        19.13         7.82         0.23        16.64        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31        19.63        19.73        14.33 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
       16.96        16.31        15.75         8.28        12.46        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N 
       49.32        66.71        67.73         2.20        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       12.46        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23        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-5889 
       47.80        21.63        40.83        26.04        30.28        10.82 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
        3.81        40.77        80.88        51.19        74.60        34.19 
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-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92         3.68        27.65        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       16.31        81.93        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GE 
       21.34        12.36        12.76        10.55        10.09        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
        6.61        92.58        52.27        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       16.31        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.07              0.10 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           149.16            194.79 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            40.70             33.47 
[1] "0.1 - 149.2 (40.7)" "0.1 - 194.8 (33.5)"
[1] "hr=" "1.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5P GAIN MUTATED       102       25        66       42
  5P GAIN WILD-TYPE     352       78       124       62
D9V3, multiclass
           clus
vv          5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I               102               352
  STAGE II               25                78
  STAGE III              66               124
  STAGE IV               42                62
[1] 4 2
[1] TRUE
[1] "dimension of 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   106  33  92   7
  5P GAIN WILD-TYPE 374  94 166   8
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1             106               374
  T2              33                94
  T3              92               166
  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   101  12   2
  5P GAIN WILD-TYPE 222  32   4
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0             101               222
  N1              12                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"
D9V6, binary
                   cls
clus                  0   1
  5P GAIN MUTATED   173  35
  5P GAIN WILD-TYPE 373  54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED    173   35
  5P GAIN WILD-TYPE  373   54
   clus
vv  5P GAIN MUTATED 5P GAIN WILD-TYPE
  0             173               373
  1              35                54
[1] 2 2
[1] FALSE
D9V7, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    68 170
  5P GAIN WILD-TYPE 224 420
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     68  170
  5P GAIN WILD-TYPE  224  420
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              68               224
  MALE               170               420
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    77   1
  5P GAIN WILD-TYPE 331   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     77    1
  5P GAIN WILD-TYPE  331    2
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO               77               331
  YES               1                 2
[1] 2 2
[1] FALSE
D9V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5P GAIN MUTATED                    8                               195
  5P GAIN WILD-TYPE                 58                               333
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5P GAIN MUTATED                                      35
  5P GAIN WILD-TYPE                                   253
D9V10, multiclass
                                       clus
vv                                      5P GAIN MUTATED 5P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                 195               333
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              35               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"
D9V11, continuous
D9V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P GAIN MUTATED                                  0     4
  5P GAIN WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED                          15   214
  5P GAIN WILD-TYPE                       106   505
D9V13, multiclass
                                  clus
vv                                 5P GAIN MUTATED 5P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     15               106
  WHITE                                        214               505
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    11 158
  5P GAIN WILD-TYPE  31 464
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11  158
  5P GAIN WILD-TYPE   31  464
                        clus
vv                       5P GAIN MUTATED 5P GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             158               464
[1] 2 2
[1] FALSE

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  5Q GAIN MUTATED   180  72
  5Q GAIN WILD-TYPE 468 156
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
              252               624 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               72               156 
$`5Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-A3-3359 TCGA-B0-4707 
       28.11        38.47        34.29        42.97        82.32        19.73 
TCGA-B0-4712 TCGA-B0-5088 TCGA-B0-5694 TCGA-B2-5635 TCGA-BP-4158 TCGA-BP-4160 
       43.96        18.51        15.78        24.82       111.02        94.72 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4762 TCGA-BP-4799 TCGA-BP-4965 
       74.17        54.77        12.33        44.15        37.25        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4999 TCGA-BP-5009 TCGA-BP-5168 
       53.65        25.81        27.22        41.62        35.90        48.10 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4904 TCGA-CJ-6027 
       27.02        31.79        31.27        63.25       108.56       118.85 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-A4W0 TCGA-BQ-5892 TCGA-DW-7838 
       11.67        37.15        66.28        81.21        11.97        24.46 
TCGA-KL-8327 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 TCGA-KO-8404 
      137.06         3.55         0.99        52.27        42.35        10.68 
TCGA-KO-8414 TCGA-3Z-A93Z TCGA-A3-3316 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3331 
      105.60        12.66        49.08        48.59        38.99        48.82 
TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3374 
       52.93        29.92        18.44        88.37        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-A6NL TCGA-A3-A6NN TCGA-AK-3429 TCGA-AK-3430 
       18.87        65.52        22.65         0.10       109.41        15.78 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3453 TCGA-AK-3460 
      109.51        94.19        48.36        78.64        83.21        82.45 
TCGA-AK-3461 TCGA-B0-4693 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4710 
       72.89         2.53         3.62        65.10         5.98        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 
        6.64         3.25        46.59         5.52        33.50         6.02 
TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       40.44        36.53        14.93        10.09        78.44        40.70 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5077 
       27.42        53.88        29.03         2.27        20.94        43.30 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       10.95         8.05        90.87        52.54        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 
       66.05        38.63        52.73        38.43        48.82        56.98 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5710 
       85.78        86.47        80.91        71.41       149.16        79.89 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4102 TCGA-B4-5838 TCGA-B8-4146 
       89.49        91.46        35.90        31.30         5.46        16.80 
TCGA-B8-4620 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 
       25.55        23.74        27.02        24.23         6.38        48.53 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 
        0.53         4.93       101.06         0.43        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 
       54.90         0.07        93.99        62.86        44.94        31.89 
TCGA-BP-4352 TCGA-BP-4758 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 
       11.31        72.59        41.75        13.15        68.38        15.78 
TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4967 
       36.39        47.97        63.62        58.68        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4989 
       57.40        58.98        48.89        46.45        31.30         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5170 
       46.45        16.47        43.00        37.02        37.48        79.30 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5192 
        2.04        30.64         9.63        37.22        13.35        23.47 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4644 TCGA-CJ-4869 
       34.95         0.95        46.55       106.16        11.05        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 TCGA-CJ-4890 
       79.66        74.27       116.84       113.46        30.64       115.69 
TCGA-CJ-4892 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       50.01       109.84        50.24        56.35        49.97        51.29 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5676 
       49.28        50.33        54.48         3.06       131.08       133.71 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       22.32       122.83        62.10        73.35        67.00        53.42 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4853 
       85.78        73.18        66.31        78.18        74.66        25.45 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 
       63.39        93.04       107.41        63.42        58.82        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       90.54        91.69        10.85        10.22        21.76        69.96 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5986 
       22.52         2.40         1.94        12.69        67.96        12.26 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 
       53.46         3.91         4.18        10.29         2.01        19.96 
TCGA-MW-A4EC TCGA-2K-A9WE TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7997 TCGA-A4-8098 
       16.37         7.04        12.82        19.36        30.48        29.46 
TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 
        0.76        12.46         8.48         9.63        62.66        41.13 
TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-EV-5902 
       20.32         0.46         0.16        25.35         0.95        19.00 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-7130 TCGA-HE-A5NK 
       13.08         4.01        23.08         1.05        58.19        73.25 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
        2.04        18.41        99.78        99.12        14.07        41.62 

$`5Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 
       31.07       109.91        58.49        28.73        22.45        52.21 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B8-4621 
      112.80       133.94        70.68       119.38       126.05        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
        1.18         8.42        15.42        32.61         3.58        80.68 
TCGA-BP-4760 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4993 
       77.62        60.59        11.64        20.38         6.94         5.82 
TCGA-BP-4995 TCGA-BP-5006 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4642 
       45.07        27.62        62.86        49.15        44.55       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       26.93        27.65        53.26        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5568 TCGA-DV-5575 TCGA-DV-5576 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       12.16        56.84        23.90        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        35.93        37.55        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
      153.73        23.84       109.22        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.91        65.19       104.52        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 
       11.21        59.08       115.00       100.87       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       96.62        90.48        92.55        11.90        36.82         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-A3-3326 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 
       37.38        62.01         4.50        45.53        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-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A8CQ 
       18.64        28.31        20.28        33.47        15.39         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 
       11.18        10.62        29.10       117.80       122.56        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 
      112.08        68.61        46.78        40.01        94.29        37.58 
TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       38.40        12.13        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4701 
        4.57         3.48        28.47        19.00         1.38         7.82 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4818 
        2.14        58.45        15.72         0.59        45.07        16.77 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 
       54.48        29.10        68.71        45.30         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4852 
       10.52        10.29        65.29        39.45        26.07        36.85 
TCGA-B0-4945 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       70.52        11.24        11.90         7.30        25.32        15.09 
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-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5399 TCGA-B0-5402 
       30.48        41.88        52.87        51.02        46.39        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
      111.52       129.67       126.28        73.84       105.37       130.65 
TCGA-B0-5711 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
      131.15        32.61         1.68        31.96        21.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
       49.97        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 
       40.04         0.85        50.14        16.60        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 
       27.29        29.88        17.06         1.74        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
       14.17        85.51        90.28        93.34        99.85        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       23.05        77.03        62.24        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       62.07        37.25        21.21        15.62        18.48        52.24 
TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4759 
       49.08        12.23        33.99        31.33        12.30        77.98 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
        5.98        71.80        48.07        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 
       61.97        13.51        56.91        60.95        48.95        36.53 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4963 
       10.98        36.95         6.71        87.45        71.41        60.30 
TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       14.24        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       36.07        33.34        36.95        30.64        18.51        38.70 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 
       35.21        28.87         6.35        74.20        52.27        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5194 
       38.30        42.44        37.25        22.78        33.24        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 
       24.62        33.47        19.82       115.00        73.22        14.17 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 
      114.41        54.61        58.95        21.24        49.25        47.18 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4901 
       64.18        51.52        63.98        24.66        39.45        47.67 
TCGA-CJ-4905 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 
       49.18        38.56        45.14         4.57        18.81        72.00 
TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-6031 
      129.40        25.71        18.87        25.25        18.15        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35       105.93        83.90        18.77        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       58.75         6.77        14.66        79.53        23.74        18.44 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5985 
       55.33        94.45        84.30        31.10        80.19        65.65 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       14.63        22.78        62.63        12.00        18.12         6.77 
TCGA-G6-A5PC TCGA-G6-A8L8 TCGA-MM-A563 TCGA-T7-A92I TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        7.96        35.87        19.43        11.70        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 
       16.64        25.64        23.97        23.28        23.31        19.63 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 
       19.73        14.33        16.96        16.31        15.75         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU 
       12.46        70.19        49.32        66.71        67.73         2.20 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-3926 
       37.51        36.49        20.25        16.77        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E 
       20.61         1.15        43.99        22.06        17.23        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-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       30.28        10.82         7.66         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       51.19        74.60        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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75        25.22        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        10.09        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94         6.61        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        11.93        19.00        16.31        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.07              0.10 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           149.16            194.79 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           40.915            33.155 
[1] "0.1 - 149.2 (40.9)" "0.1 - 194.8 (33.2)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q GAIN MUTATED       115       25        66       44
  5Q GAIN WILD-TYPE     339       78       124       60
D10V3, multiclass
           clus
vv          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I               115               339
  STAGE II               25                78
  STAGE III              66               124
  STAGE IV               44                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   120  33  94   6
  5Q GAIN WILD-TYPE 360  94 164   9
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1             120               360
  T2              33                94
  T3              94               164
  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   110  12   2
  5Q GAIN WILD-TYPE 213  32   4
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0             110               213
  N1              12                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"
D10V6, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED   187  37
  5Q GAIN WILD-TYPE 359  52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED    187   37
  5Q GAIN WILD-TYPE  359   52
   clus
vv  5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  0             187               359
  1              37                52
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    73 180
  5Q GAIN WILD-TYPE 219 410
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     73  180
  5Q GAIN WILD-TYPE  219  410
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              73               219
  MALE               180               410
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    85   1
  5Q GAIN WILD-TYPE 323   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     85    1
  5Q GAIN WILD-TYPE  323    2
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO               85               323
  YES               1                 2
[1] 2 2
[1] FALSE
D10V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5Q GAIN MUTATED                    8                               213
  5Q GAIN WILD-TYPE                 58                               315
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5Q GAIN MUTATED                                      32
  5Q GAIN WILD-TYPE                                   256
D10V10, multiclass
                                       clus
vv                                      5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                 213               315
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              32               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"
D10V11, continuous
D10V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q GAIN MUTATED                                  0     4
  5Q GAIN WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED                          18   226
  5Q GAIN WILD-TYPE                       103   493
D10V13, multiclass
                                  clus
vv                                 5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     18               103
  WHITE                                        226               493
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    11 172
  5Q GAIN WILD-TYPE  31 450
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     11  172
  5Q GAIN WILD-TYPE   31  450
                        clus
vv                       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             172               450
[1] 2 2
[1] FALSE

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                 0   1
  6P GAIN MUTATED    13   9
  6P GAIN WILD-TYPE 635 219
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               22               854 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                9               219 
$`6P GAIN MUTATED`
TCGA-BP-4799 TCGA-AL-A5DJ TCGA-DW-5561 TCGA-KM-8639 TCGA-KN-8427 TCGA-A3-3313 
       37.25        49.25        13.61        31.33         0.99        24.16 
TCGA-B0-4811 TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 TCGA-BP-4985 TCGA-BP-5177 
       46.59        38.63         6.38        68.38        31.30         9.63 
TCGA-CJ-4885 TCGA-CZ-5460 TCGA-4A-A93X TCGA-AL-3466 TCGA-B9-A69E TCGA-BQ-5893 
      113.46        94.45        12.82         9.63        14.86         7.92 
TCGA-BQ-7048 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       93.34         6.61        14.07        86.27 

$`6P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       11.64        20.38         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        12.99        76.64        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.28        48.85       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 
      151.96        44.91        49.97       123.12        51.06       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-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       99.88       105.60        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       11.90        36.82         0.53        39.16        49.08        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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-B0-4813 
       57.70         6.64         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        5.52        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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        46.45        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       30.64        52.27        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        61.91        57.83        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23         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-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         0.95         2.76       123.62        48.26 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS 
      117.40       103.63       125.29        37.35        98.96        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.99              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           113.46            194.79 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            27.73             36.00 
[1] "1.0 - 113.5 (27.7)" "0.1 - 194.8 (36.0)"
[1] "hr=" "1.9"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P GAIN MUTATED         6        0        10        6
  6P GAIN WILD-TYPE     448      103       180       98
D11V3, multiclass
           clus
vv          6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                 6               448
  STAGE II                0               103
  STAGE III              10               180
  STAGE IV                6                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
  6P GAIN MUTATED     6   1  14   1
  6P GAIN WILD-TYPE 474 126 244  14
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               6               474
  T2               1               126
  T3              14               244
  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     7   6   0
  6P GAIN WILD-TYPE 316  38   6
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0               7               316
  N1               6                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    10   4
  6P GAIN WILD-TYPE 536  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     10    4
  6P GAIN WILD-TYPE  536   85
   clus
vv  6P GAIN MUTATED 6P GAIN WILD-TYPE
  0              10               536
  1               4                85
[1] 2 2
[1] FALSE
D11V7, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     5  17
  6P GAIN WILD-TYPE 287 573
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      5   17
  6P GAIN WILD-TYPE  287  573
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE               5               287
  MALE                17               573
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    11   0
  6P GAIN WILD-TYPE 397   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     11    0
  6P GAIN WILD-TYPE  397    3
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO               11               397
  YES               0                 3
[1] 2 2
[1] FALSE
D11V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6P GAIN MUTATED                    2                                10
  6P GAIN WILD-TYPE                 64                               518
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6P GAIN MUTATED                                      10
  6P GAIN WILD-TYPE                                   278
D11V10, multiclass
                                       clus
vv                                      6P GAIN MUTATED 6P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  2                64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  10               518
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              10               278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
D11V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P GAIN MUTATED                                  0     0
  6P GAIN WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED                           4    18
  6P GAIN WILD-TYPE                       117   701
D11V13, multiclass
                                  clus
vv                                 6P GAIN MUTATED 6P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                16
  BLACK OR AFRICAN AMERICAN                      4               117
  WHITE                                         18               701
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V14, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     0  16
  6P GAIN WILD-TYPE  42 606
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      0   16
  6P GAIN WILD-TYPE   42  606
                        clus
vv                       6P GAIN MUTATED 6P GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO              16               606
[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 640 220
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               16               860 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                8               220 
$`6Q GAIN MUTATED`
TCGA-BP-4799 TCGA-AL-A5DJ TCGA-DW-5561 TCGA-KM-8639 TCGA-A3-3313 TCGA-B0-4811 
       37.25        49.25        13.61        31.33        24.16        46.59 
TCGA-B0-5113 TCGA-B8-5549 TCGA-BP-4781 TCGA-BP-4985 TCGA-CJ-4885 TCGA-4A-A93X 
       38.63         6.38        68.38        31.30       113.46        12.82 
TCGA-AL-3466 TCGA-BQ-5893 TCGA-P4-A5EA TCGA-Q2-A5QZ 
        9.63         7.92         6.61        14.07 

$`6Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       11.64        20.38         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        12.99        76.64        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.28        48.85       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 
      151.96        44.91        49.97       123.12        51.06       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.55         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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-3430 
       10.62        29.10       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       19.30        66.05        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        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        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
       10.82         5.33        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91        57.83        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-3471 
       16.31        15.75         8.28        12.46        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             6.38              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           113.46            194.79 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            27.73             36.00 
[1] "6.4 - 113.5 (27.7)" "0.1 - 194.8 (36.0)"
[1] "hr=" "2.7"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q GAIN MUTATED         5        0         7        4
  6Q GAIN WILD-TYPE     449      103       183      100
D12V3, multiclass
           clus
vv          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                 5               449
  STAGE II                0               103
  STAGE III               7               183
  STAGE IV                4               100
[1] 4 2
[1] TRUE
[1] "dimension of 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   0  11   0
  6Q GAIN WILD-TYPE 475 127 247  15
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               5               475
  T2               0               127
  T3              11               247
  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     6   4   0
  6Q GAIN WILD-TYPE 317  40   6
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0               6               317
  N1               4                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"
D12V6, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8   3
  6Q GAIN WILD-TYPE 538  86
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    3
  6Q GAIN WILD-TYPE  538   86
   clus
vv  6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  0               8               538
  1               3                86
[1] 2 2
[1] FALSE
D12V7, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     4  12
  6Q GAIN WILD-TYPE 288 578
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   12
  6Q GAIN WILD-TYPE  288  578
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE               4               288
  MALE                12               578
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     8   0
  6Q GAIN WILD-TYPE 400   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      8    0
  6Q GAIN WILD-TYPE  400    3
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                8               400
  YES               0                 3
[1] 2 2
[1] FALSE
D12V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6Q GAIN MUTATED                    1                                 8
  6Q GAIN WILD-TYPE                 65                               520
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6Q GAIN MUTATED                                       7
  6Q GAIN WILD-TYPE                                   281
D12V10, multiclass
                                       clus
vv                                      6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   8               520
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
D12V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q GAIN MUTATED                                  0     0
  6Q GAIN WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED                           3    13
  6Q GAIN WILD-TYPE                       118   706
D12V13, multiclass
                                  clus
vv                                 6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                16
  BLACK OR AFRICAN AMERICAN                      3               118
  WHITE                                         13               706
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V14, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     0  12
  6Q GAIN WILD-TYPE  42 610
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      0   12
  6Q GAIN WILD-TYPE   42  610
                        clus
vv                       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO              12               610
[1] 2 2
[1] FALSE

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                 0   1
  7P GAIN MUTATED   277  88
  7P GAIN WILD-TYPE 371 140
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              365               511 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               88               140 
$`7P GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4707 
       28.11        38.47        34.29        42.97       109.91        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5694 TCGA-B0-5698 TCGA-B8-4621 TCGA-BP-4158 
       43.96        52.21        15.78       119.38        25.91       111.02 
TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5201 TCGA-CJ-4636 
       60.59        37.25        35.90        62.86        31.27        63.25 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-DV-5565 TCGA-DV-5574 TCGA-G6-A8L7 TCGA-2Z-A9JD 
      103.43        46.16        43.69        66.28        70.13        34.85 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 
       33.07        25.58        16.18        22.49        12.26        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 
       21.37         0.89        76.64        49.25        21.67        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 
       10.16        21.86        19.23        96.92        48.85        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-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 
        3.02        61.02        17.95        84.89        16.34        17.75 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8324 
       62.83        86.37        21.60        15.91        15.62       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8346 TCGA-KM-8438 
      137.06        98.96        24.79        71.41        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-8404 TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 
       11.21        42.35        10.68       100.47        16.67       104.55 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       99.88       105.60        96.62        24.16        49.08        49.02 
TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3347 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
       48.59        38.99        52.93        10.49        24.16        43.20 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-AK-3427 
       18.87        65.52        20.28         0.10        11.18       117.80 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
      109.41        15.78       112.08       109.51        94.19        48.36 
TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4696 
       83.21         3.32         1.41         4.57         3.48        28.47 
TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4839 
       57.70         3.25        46.59        10.09        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5102 
        6.71        36.85        43.30        10.95         2.24        90.87 
TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 
       19.30        38.63        41.88        80.91        73.84        91.46 
TCGA-B2-3924 TCGA-B2-5633 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 
       35.90        31.66         5.10         0.53         5.46         0.36 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I 
       17.19        25.55        50.14        48.53        29.88         4.93 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 
       85.51       101.06         0.43        89.36        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       61.78        64.27        97.45        37.25        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4759 
       93.99        62.86        31.89        11.31        33.99        77.98 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4790 
       48.07        13.15         5.33        68.38        15.78        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 
       36.39        10.98         6.71        47.97        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 
       60.30         6.74        58.98        48.89        45.50        14.93 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 
       46.45        31.30        36.95         3.88        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5177 
       30.64        38.70         6.35        79.30         2.04         9.63 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4644 TCGA-CJ-4870 
       19.82        34.95        46.55        14.17        11.05        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4887 
       79.66        47.18        74.27       116.84       113.46        30.64 
TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       63.98       109.84        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       131.08        72.00        22.32       122.83        73.35 
TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4857 TCGA-CZ-4858 
       53.42        66.31        74.66         1.35        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 
        6.77       107.41        79.53        23.74        79.63        90.54 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       94.45        10.85        69.96        22.52         1.94        31.10 
TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-MM-A564 TCGA-2K-A9WE TCGA-2Z-A9J1 
       67.96        62.63        53.46        19.96         7.04        75.55 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JM 
       58.22       100.27        56.91         4.57        56.81        30.71 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K0 
       29.36         5.29         0.13        12.82        49.58        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KC TCGA-5P-A9KE 
       78.64        71.80        62.93        19.36        12.39        27.09 
TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
       19.13        16.64        30.48        25.64        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU 
        0.76        19.63        14.33        16.96         8.48        16.31 
TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU 
       15.75        12.46        49.32        66.71        67.73         2.20 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
       36.49        20.25        20.32        33.83        30.58        12.46 
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-A8YH TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 
       22.06        17.49        47.80        26.04        25.35        10.82 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7059 
        0.95         2.76       123.62        48.26        50.40         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
       34.19        24.89        13.08         2.40         1.18         4.01 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       51.78        39.25        25.84        25.25        17.98        23.08 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DD 
       80.65       194.79         3.68        27.65        12.43        11.21 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       81.93        58.19        26.01        11.84        56.75        25.22 
TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
        2.04        88.24        96.69        21.34        12.36        12.76 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 
       18.41        29.10        11.41        34.29        27.78        20.25 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVK TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71R 
       15.48        87.09        52.27        16.01        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       49.45        44.61        28.80        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
      125.29        37.35        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       51.35        31.73        18.64        25.28         6.02 

$`7P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5088 
       31.07        82.32        58.49        28.73        22.45        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 
      112.80       133.94        70.68       126.05        24.82         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 
       74.17        54.77        12.33        77.62        44.15        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       20.38         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 
        5.82        45.07        41.62        27.62        48.10        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       27.02        31.79        44.55       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56        53.26       118.85        75.58         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        5.46        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JJ 
       56.84        23.90        81.21        23.01        75.42        39.88 
TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 
       67.17        12.99        27.68        11.87        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 
       11.97        44.84        26.27        20.12        11.28        13.78 
TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ 
       67.17        12.13        29.26        19.73        41.33         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07        23.84       109.22        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 
       66.54        73.91        28.80        54.74        44.91       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-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8416 
      100.87       105.47       103.40        92.71       103.10        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       92.55        12.66        11.90        36.82         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        62.01 
TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
        4.50        45.53        29.92        18.44        88.37        51.25 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       18.64        28.31        33.47        15.39        22.65         0.10 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 
       10.62        29.10       122.56        73.68        68.61        46.78 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        40.01        94.29        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 
       72.89        12.13        40.70         1.41         2.53        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-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        6.64        58.45        15.72         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-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        78.44        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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 
       29.03         2.27        70.52        20.94        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 TCGA-B0-5098 
        7.30        25.32        15.09         8.05        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        58.59 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       86.47       126.28        71.41       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
       79.89       131.15        89.49        32.61         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       21.30        31.30        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        5.75         1.25         4.64         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 
       49.97        42.71        25.05        45.37        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5551 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-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 
       17.36        16.27        14.17        90.28        93.34        99.85 
TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4334 
       23.05        54.90        53.42        27.78        62.07        21.21 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 
       18.48        52.24        49.08        44.94        12.23        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 
       12.30        72.59         5.98        41.75        71.80        61.68 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
       10.82        61.97        13.51        56.91        60.95        48.95 
TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 
       36.95        87.45        63.62        61.22        57.40        14.24 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4991 
       49.38         6.94        47.11        36.07        33.34        46.45 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5174 
       18.51        37.02        37.48        35.21        28.87        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       30.64        52.27        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 
       24.62        33.47         0.95       115.00        73.22       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4874 
      114.41        54.61        58.95        21.24        83.97        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-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       51.52       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
       56.35        49.97        49.18        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
        3.06        18.81       129.40       133.71        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
       25.25        18.15        62.10        67.00        62.66       119.64 
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-6097 TCGA-CZ-4853 
       73.18        78.18       105.93        83.90        18.77        25.45 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       18.44        91.69        55.33        10.22        21.76        84.30 
TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40        12.69        80.19        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC 
        7.96        10.29        35.87         2.01        19.43        16.37 
TCGA-T7-A92I TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
       11.70        59.01        91.73        54.64        51.52        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 
       24.33        31.20        11.57       106.55        90.21        15.48 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       43.04        12.99        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 
       35.18         7.82         0.23        29.46        23.28        19.73 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
       12.46         8.28         9.63        70.19        62.66        41.13 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A5W8 
       37.51        16.77        29.03        34.49        20.61        17.23 
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-5890 TCGA-BQ-5893 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-DZ-6131 
        7.66         7.92        93.34        61.28        49.84        79.86 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 
       74.60        19.00        10.68         0.43        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM 
       71.44        25.15        20.52        16.90        12.92         1.05 
TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       12.89        16.31        73.25        16.80        19.99        85.78 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 
       22.26        10.55        10.09        30.38        27.65        17.62 
TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       31.13        99.78        42.94         6.61        99.12        92.58 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PL TCGA-UZ-A9PP 
       50.60        78.90        27.06        18.02       103.63        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 
       86.27        71.24        26.01        39.06        18.64        18.05 
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            149.16 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            33.99             37.15 
[1] "0.1 - 194.8 (34.0)" "0.1 - 149.2 (37.1)"
[1] "hr=" "1.1"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P GAIN MUTATED       190       40        70       51
  7P GAIN WILD-TYPE     264       63       120       53
D13V3, multiclass
           clus
vv          7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I               190               264
  STAGE II               40                63
  STAGE III              70               120
  STAGE IV               51                53
[1] 4 2
[1] TRUE
[1] "dimension of 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   202  53 106   7
  7P GAIN WILD-TYPE 278  74 152   8
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1             202               278
  T2              53                74
  T3             106               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   121  20   4
  7P GAIN WILD-TYPE 202  24   2
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0             121               202
  N1              20                24
  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"
D13V6, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   193  43
  7P GAIN WILD-TYPE 353  46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    193   43
  7P GAIN WILD-TYPE  353   46
   clus
vv  7P GAIN MUTATED 7P GAIN WILD-TYPE
  0             193               353
  1              43                46
[1] 2 2
[1] FALSE
D13V7, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    88 281
  7P GAIN WILD-TYPE 204 309
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     88  281
  7P GAIN WILD-TYPE  204  309
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              88               204
  MALE               281               309
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                  0   1
  7P GAIN MUTATED   185   2
  7P GAIN WILD-TYPE 223   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED    185    2
  7P GAIN WILD-TYPE  223    1
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO              185               223
  YES               2                 1
[1] 2 2
[1] FALSE
D13V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7P GAIN MUTATED                   24                               173
  7P GAIN WILD-TYPE                 42                               355
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7P GAIN MUTATED                                     172
  7P GAIN WILD-TYPE                                   116
D13V10, multiclass
                                       clus
vv                                      7P GAIN MUTATED 7P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                 173               355
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             172               116
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
D13V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P GAIN MUTATED                                  2     8
  7P GAIN WILD-TYPE                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED                          44   302
  7P GAIN WILD-TYPE                        77   417
D13V13, multiclass
                                  clus
vv                                 7P GAIN MUTATED 7P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          8                 8
  BLACK OR AFRICAN AMERICAN                     44                77
  WHITE                                        302               417
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V14, binary
                   cls
clus                  0   1
  7P GAIN MUTATED    15 267
  7P GAIN WILD-TYPE  27 355
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     15  267
  7P GAIN WILD-TYPE   27  355
                        clus
vv                       7P GAIN MUTATED 7P GAIN WILD-TYPE
  HISPANIC OR LATINO                  15                27
  NOT HISPANIC OR LATINO             267               355
[1] 2 2
[1] FALSE

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                 0   1
  7Q GAIN MUTATED   276  91
  7Q GAIN WILD-TYPE 372 137
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
              367               509 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               91               137 
$`7Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4707 
       28.11        38.47        34.29        42.97       109.91        19.73 
TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5694 TCGA-B0-5698 TCGA-B8-4621 TCGA-BP-4158 
       43.96        52.21        15.78       119.38        25.91       111.02 
TCGA-BP-4775 TCGA-BP-4799 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5201 TCGA-CJ-4636 
       60.59        37.25        35.90        62.86        31.27        63.25 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-DV-5565 TCGA-DV-5574 TCGA-G6-A8L7 TCGA-2Z-A9JD 
      103.43        46.16        43.69        66.28        70.13        34.85 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 
       33.07        25.58        16.18        22.49        12.26        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 
       21.37         0.89        76.64        49.25        21.67        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5560 
       10.16        21.86        19.23        11.97        96.92        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        24.46         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       14.63         3.02        61.02        17.95        84.89        16.34 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        62.83        86.37        21.60        15.91        15.62 
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8346 
      153.73       137.06        98.96        24.79        71.41        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
      151.96        49.97        23.47        25.91       104.52         3.55 
TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8408 
       52.27        11.21        42.35        10.68       100.47        16.67 
TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3316 
      104.55        99.88       105.60        96.62        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3347 TCGA-A3-3363 TCGA-A3-3372 
       49.02        48.59        38.99        52.93        10.49        24.16 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OV 
       43.20        18.87        65.52        20.28         0.10        11.18 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 
      117.80       109.41        15.78       112.08       109.51        94.19 
TCGA-AK-3444 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       48.36        83.21         3.32         1.41         4.57         3.48 
TCGA-B0-4696 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 
       28.47        57.70         3.25        46.59         6.02        10.09 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4852 TCGA-B0-5077 TCGA-B0-5094 
       27.42        53.88         6.71        36.85        43.30        10.95 
TCGA-B0-5096 TCGA-B0-5102 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5701 
        2.24        90.87        19.30        38.63        41.88        80.91 
TCGA-B0-5703 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 
       73.84        91.46        35.90        32.98         5.10         0.53 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
        5.46         0.36        16.80        17.19        25.55        50.14 
TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4166 
       48.53        29.88         4.93        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        15.62         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-4781 TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 
       68.38        15.78        36.53        10.98         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 
       71.41        58.68        60.30         6.74        58.98        48.89 
TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       45.50        14.93        46.45        31.30        36.95         3.88 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       16.47        43.00        30.64         6.35        79.30         2.04 
TCGA-BP-5177 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4644 
        9.63        19.82        34.95        46.55        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       116.84       113.46        30.64 
TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       63.98       109.84        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       131.08        72.00        25.71        22.32       122.83 
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-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5454 
       18.77        47.08        69.21         6.77       107.41        23.74 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
       79.63        90.54        94.45        10.85        69.96        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-MM-A564 
        1.94        31.10        67.96        62.63        53.46        19.96 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        58.22       100.27        56.91         4.57 
TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       56.81        30.71        29.36         5.29         0.13        12.82 
TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       49.58        22.26        78.64        71.80        62.93        19.36 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       12.39        27.09        19.13        16.64        30.48        25.64 
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-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-3472 
        8.48        16.31        15.75        12.46        49.32        66.71 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 
       67.73         2.20        36.49        20.25        20.32        33.83 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       30.58        12.46        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5884 
        1.15        43.99        22.06        17.49        47.80        26.04 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
       25.35        10.82         0.95         2.76       123.62        48.26 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       50.40         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       80.88        51.19        34.19        24.89        13.08         2.40 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM 
        1.18         4.01        51.78        39.25        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       17.98        23.08        80.65       194.79         3.68        27.65 
TCGA-GL-A59R TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.43        11.21        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 
       56.75        25.22         2.04        88.24        96.69        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.36        12.76        18.41        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        87.09        52.27        16.01 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM 
       14.07        47.90        49.45        44.61        28.80        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PU TCGA-UZ-A9PV 
       26.20       117.40       125.29        37.35        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A896 TCGA-Y8-A8RY 
       65.13       110.73        51.35        31.73        18.64        25.28 
TCGA-Y8-A8S0 
        6.02 

$`7Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5088 
       31.07        82.32        58.49        28.73        22.45        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 
      112.80       133.94        70.68       126.05        24.82         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 
       74.17        54.77        12.33        77.62        44.15        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       20.38         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 
        5.82        45.07        41.62        27.62        48.10        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       27.02        31.79        44.55       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4856 TCGA-CZ-4862 
      108.56        53.26       118.85        75.58         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        5.46        45.96        65.88        12.16        11.67        37.15 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JJ 
       56.84        23.90        81.21        23.01        75.42        39.88 
TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 
       67.17        12.99        27.68        11.87        26.04        13.25 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-7839 TCGA-IA-A83W 
       44.84        26.27        20.12        11.28        13.78        67.17 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-KL-8323 
       12.13        29.26        19.73        41.33         6.74        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 
       23.84       109.22        90.48       108.62        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8342 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 
       73.91        28.80        54.74        44.91       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8427 
       31.33       129.37        87.91        25.48        65.19         0.99 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 
       87.12        19.33         2.50        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8416 TCGA-KO-8417 
      105.47       103.40        92.71       103.10        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3319 
       12.66        11.90        36.82         0.53        39.16        37.15 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       49.58        36.36        37.38        48.82        62.01         4.50 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 
       45.53        29.92        18.44        88.37        51.25        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OW 
       28.31        33.47        15.39        22.65         0.10        10.62 
TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 
       29.10       122.56        73.68        68.61        46.78        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       40.01        94.29        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4698 
       12.13        40.70         1.41         2.53        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 
        3.62        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77        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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       70.52        20.94        11.24        11.90         7.30        25.32 
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        58.59        66.05        52.73 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       71.41       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       89.49        32.61         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       31.66        21.57        16.67        12.00         5.75         1.25 
TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        4.64         0.23        23.31        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       45.37        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       50.14        16.60         6.38         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       27.29        17.06         1.74        17.36        16.27        14.17 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 
       90.28        93.34        99.85        23.05        54.90        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 
       27.78        62.07        21.21        18.48        52.24        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4761 
       44.94        12.23        31.33        12.30        72.59         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 
       41.75        71.80        61.68        10.82        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4959 
       56.91        60.95        48.95        36.39        36.95        87.45 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4974 
       63.62        61.22        57.40        14.24        49.38         6.94 
TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4991 TCGA-BP-5000 TCGA-BP-5001 
       47.11        36.07        33.34        46.45        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5174 TCGA-BP-5175 
       37.02        37.48        35.21        28.87        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       52.27        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 
       33.47         0.95       115.00        73.22       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 
       54.61        58.95        21.24        83.97        49.25        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-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       51.52       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 
       56.35        49.97        49.18        50.33        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
        3.06        18.81       129.40       133.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       18.15        67.00        62.66       119.64         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-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
      105.93        83.90        25.45        58.75        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5458 
       93.04        63.42        58.82        79.53        18.44        91.69 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 
       55.33        10.22        21.76        84.30         2.40        12.69 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-A4VZ 
       80.19        65.65        12.26        14.63        22.78        12.00 
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-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J2 
       35.87         2.01        19.43        16.37        11.70        59.01 
TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        54.64        51.52        38.99        24.33        31.20 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA 
       11.57       106.55        90.21        15.48        43.04        12.99 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 
       67.43        18.21        19.63         0.10        35.18         7.82 
TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 
        0.23        29.46        23.28        19.73        12.46         8.28 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 
        9.63        70.19        62.66        41.13        37.51        16.77 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
       29.03        34.49        20.61        17.23         0.16        14.86 
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-5882 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5893 
       43.20        21.63        40.83        30.28         7.66         7.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 
       93.34        61.28        49.84        79.86        74.60        19.00 
TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 
       10.68         0.43        90.90        11.05        71.44        25.15 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE 
       20.52        16.90        12.92         1.05        12.89        16.31 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IZ-8195 TCGA-J7-8537 
       73.25        16.80        19.99        85.78        22.26        10.55 
TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 
       10.09        30.38        27.65        17.62        31.13        99.78 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO 
       42.94         6.61        99.12        92.58        50.60        78.90 
TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
       27.06        18.02       103.63        98.96        86.27        71.24 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8S1 
       26.01        39.06        18.64        18.05        13.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.10 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           194.79            149.16 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            31.89             37.25 
[1] "0.1 - 194.8 (31.9)" "0.1 - 149.2 (37.2)"
[1] "hr=" "1"  
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q GAIN MUTATED       191       39        69       54
  7Q GAIN WILD-TYPE     263       64       121       50
D14V3, multiclass
           clus
vv          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I               191               263
  STAGE II               39                64
  STAGE III              69               121
  STAGE IV               54                50
[1] 4 2
[1] TRUE
[1] "dimension of 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   203  52 108   7
  7Q GAIN WILD-TYPE 277  75 150   8
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1             203               277
  T2              52                75
  T3             108               150
  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   120  20   4
  7Q GAIN WILD-TYPE 203  24   2
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0             120               203
  N1              20                24
  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"
D14V6, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   192  46
  7Q GAIN WILD-TYPE 354  43
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    192   46
  7Q GAIN WILD-TYPE  354   43
   clus
vv  7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  0             192               354
  1              46                43
[1] 2 2
[1] FALSE
D14V7, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    89 282
  7Q GAIN WILD-TYPE 203 308
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     89  282
  7Q GAIN WILD-TYPE  203  308
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              89               203
  MALE               282               308
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED   185   3
  7Q GAIN WILD-TYPE 223   0
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED    185    3
  7Q GAIN WILD-TYPE  223    0
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO              185               223
  YES               3                 0
[1] 2 2
[1] FALSE
D14V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7Q GAIN MUTATED                   24                               174
  7Q GAIN WILD-TYPE                 42                               354
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7Q GAIN MUTATED                                     173
  7Q GAIN WILD-TYPE                                   115
D14V10, multiclass
                                       clus
vv                                      7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 24                42
  KIDNEY CLEAR CELL RENAL CARCINOMA                 174               354
  KIDNEY PAPILLARY RENAL CELL CARCINOMA             173               115
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
D14V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q GAIN MUTATED                                  2     8
  7Q GAIN WILD-TYPE                                0     8
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED                          43   305
  7Q GAIN WILD-TYPE                        78   414
D14V13, multiclass
                                  clus
vv                                 7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          8                 8
  BLACK OR AFRICAN AMERICAN                     43                78
  WHITE                                        305               414
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V14, binary
                   cls
clus                  0   1
  7Q GAIN MUTATED    15 270
  7Q GAIN WILD-TYPE  27 352
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     15  270
  7Q GAIN WILD-TYPE   27  352
                        clus
vv                       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  HISPANIC OR LATINO                  15                27
  NOT HISPANIC OR LATINO             270               352
[1] 2 2
[1] FALSE

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                 0   1
  8P GAIN MUTATED    47  21
  8P GAIN WILD-TYPE 601 207
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               68               808 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               21               207 
$`8P GAIN MUTATED`
TCGA-KL-8339 TCGA-BP-4342 TCGA-BP-5191 TCGA-B1-A47O TCGA-BQ-7056 TCGA-KL-8324 
       28.11        74.17        31.79        27.68        20.12       153.73 
TCGA-KL-8331 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 
       98.96        62.37       151.96        49.97        23.47        25.91 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 
        0.99        52.27        11.21       100.47       104.55       103.10 
TCGA-KO-8413 TCGA-A3-3313 TCGA-A3-3316 TCGA-AK-3433 TCGA-AK-3445 TCGA-B0-4713 
       99.88        24.16        49.08       112.08        78.64         6.64 
TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5097 TCGA-B0-5109 TCGA-B4-5832 
       40.44        10.09        10.29        21.86        19.30         5.10 
TCGA-BP-4768 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5185 TCGA-CJ-4871 
       13.15        46.45        31.30        18.51        37.22        79.66 
TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CJ-4923 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 
       66.21        47.67        18.81        66.31        74.66        69.21 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 
      107.41        79.63        69.96        31.10        12.69        14.63 
TCGA-DV-A4VX TCGA-MM-A564 TCGA-2Z-A9J2 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9K9 
       53.46        19.96        59.01        29.36        12.82        19.36 
TCGA-A4-8630 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-G7-6789 
       14.33        49.32         0.16        43.20        25.35         4.01 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-SX-A71U 
        3.68         1.05        22.26         6.61        16.01        44.61 
TCGA-SX-A7SR TCGA-V9-A7HT 
       26.47        31.73 

$`8P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       62.86        49.15        27.02        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        49.25        21.67        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       96.92        44.84        26.27        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       137.06        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-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       54.74        44.91       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 
       87.91        25.48        65.19       104.52         3.55        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-8414 
      105.47        10.68       103.40        92.71        16.67       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       96.62        90.48        92.55        12.66        11.90        36.82 
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
        0.53        39.16        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
      109.41        15.78        73.68        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       46.78        48.36        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        2.14        57.70         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 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 
       10.52        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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        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        58.59        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-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-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 
       47.11        14.93        36.07        33.34        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        43.00        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       50.24        56.35        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
       58.75         6.77        14.66        63.39        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
       22.52         2.40         1.94        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       12.26        22.78        62.63        12.00        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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 
       19.43        16.37        11.70         7.04        75.55        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR 
       51.52        38.99        30.71        24.33        31.20         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-A6HP TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E 
        0.46         1.15        43.99        22.06        17.23        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-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       12.92        27.65        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       96.69        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM 
       87.09        42.94        99.12        92.58        52.27        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        14.07        47.90        49.45        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-SX-A7SU 
       11.93        19.00        16.31        41.62        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.16              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           153.73            194.79 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           31.200            36.215 
[1] "0.2 - 153.7 (31.2)" "0.1 - 194.8 (36.2)"
[1] "hr=" "1.2"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P GAIN MUTATED        18       19        19       12
  8P GAIN WILD-TYPE     436       84       171       92
D15V3, multiclass
           clus
vv          8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                18               436
  STAGE II               19                84
  STAGE III              19               171
  STAGE IV               12                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
  8P GAIN MUTATED    18  20  30   1
  8P GAIN WILD-TYPE 462 107 228  14
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1              18               462
  T2              20               107
  T3              30               228
  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    30   7   2
  8P GAIN WILD-TYPE 293  37   4
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              30               293
  N1               7                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"
D15V6, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    37   8
  8P GAIN WILD-TYPE 509  81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     37    8
  8P GAIN WILD-TYPE  509   81
   clus
vv  8P GAIN MUTATED 8P GAIN WILD-TYPE
  0              37               509
  1               8                81
[1] 2 2
[1] FALSE
D15V7, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    23  46
  8P GAIN WILD-TYPE 269 544
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     23   46
  8P GAIN WILD-TYPE  269  544
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              23               269
  MALE                46               544
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    35   0
  8P GAIN WILD-TYPE 373   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     35    0
  8P GAIN WILD-TYPE  373    3
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO               35               373
  YES               0                 3
[1] 2 2
[1] FALSE
D15V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8P GAIN MUTATED                   16                                33
  8P GAIN WILD-TYPE                 50                               495
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8P GAIN MUTATED                                      20
  8P GAIN WILD-TYPE                                   268
D15V10, multiclass
                                       clus
vv                                      8P GAIN MUTATED 8P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 16                50
  KIDNEY CLEAR CELL RENAL CARCINOMA                  33               495
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              20               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"
D15V11, continuous
D15V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P GAIN MUTATED                                  0     2
  8P GAIN WILD-TYPE                                2    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED                           5    61
  8P GAIN WILD-TYPE                       116   658
D15V13, multiclass
                                  clus
vv                                 8P GAIN MUTATED 8P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          2                14
  BLACK OR AFRICAN AMERICAN                      5               116
  WHITE                                         61               658
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V14, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     3  48
  8P GAIN WILD-TYPE  39 574
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      3   48
  8P GAIN WILD-TYPE   39  574
                        clus
vv                       8P GAIN MUTATED 8P GAIN WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              48               574
[1] 2 2
[1] FALSE

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                 0   1
  8Q GAIN MUTATED    67  35
  8Q GAIN WILD-TYPE 581 193
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
              102               774 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               35               193 
$`8Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3336 TCGA-AK-3425 TCGA-B0-4712 TCGA-BP-4342 TCGA-BP-4799 
       28.11        34.29       109.91        43.96        74.17        37.25 
TCGA-BP-5191 TCGA-CZ-4854 TCGA-BQ-7056 TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8346 
       31.79        46.16        20.12       153.73        98.96        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-8433 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       52.27        11.21       100.47       104.55       103.10        99.88 
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-AK-3433 TCGA-AK-3434 
        0.53        24.16        49.08        37.15       112.08        68.61 
TCGA-AK-3445 TCGA-B0-4688 TCGA-B0-4713 TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-4844 
       78.64         3.32         6.64        40.44        10.09        10.29 
TCGA-B0-5081 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5109 TCGA-B4-5832 TCGA-B8-5158 
       11.90        21.86        58.59        19.30         5.10        40.04 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 TCGA-BP-4761 TCGA-BP-4768 
       27.02         0.53         4.93        61.78         5.98        13.15 
TCGA-BP-4798 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-5000 TCGA-BP-5169 
       10.98        58.68        46.45        31.30        18.51         6.35 
TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5185 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4901 
        2.04        30.64        37.22        79.66        66.21        47.67 
TCGA-CJ-4912 TCGA-CJ-4923 TCGA-CJ-5677 TCGA-CJ-6033 TCGA-CW-5588 TCGA-CW-5591 
       54.48        18.81        25.71         7.36        66.31        74.66 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 
       69.21       107.41        79.63        10.22        69.96        22.52 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-MM-A564 
        1.94        31.10        12.69        14.63        53.46        19.96 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-8630 
       59.01        58.22        29.36        12.82        19.36        14.33 
TCGA-AL-3466 TCGA-AL-3471 TCGA-B9-A5W9 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-F9-A8NY 
        9.63        49.32         0.16        43.20        25.35         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 TCGA-V9-A7HT 
        6.61        16.01        14.07        44.61        26.47        31.73 

$`8Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 
       38.47        31.07        42.97        82.32        58.49        28.73 
TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       22.45        19.73        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 
        3.58        80.68        54.77        12.33        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       60.59        11.64        20.38         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 
       35.90        48.10        62.86        49.15        27.02        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 
       13.25        11.97        96.92        44.84        26.27        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
       15.62         6.74        38.07        23.84       109.22       137.06 
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-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 
       71.41        28.80        54.74        44.91       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-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       105.47        10.68       103.40        92.71        16.67 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       36.82        39.16        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68       109.51        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         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-B0-4710 TCGA-B0-4714 
       65.10         7.82         5.98         2.14        57.70         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 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-B0-4845 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       90.48        52.54        30.48        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       25.55        50.14        23.74         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60         6.38        48.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       29.88        17.06         1.74        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 
       89.36        23.05        77.03        62.24        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        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-4343 
       15.62         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 
       31.33        12.30        72.59        77.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       36.39        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       63.62        60.30        61.22         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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       14.93        36.07        33.34        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        43.00        30.64        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 
       35.21        28.87        79.30        74.20        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
       74.40        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       83.97        49.25        47.18        74.27        75.06       116.84 
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       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        50.24        56.35        49.97        51.29 
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       131.08        72.00       129.40       133.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 TCGA-CW-5581 
       67.00        53.42        62.66       119.64        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 
       81.83         5.39        85.78        73.18        78.18         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 
      105.93        83.90        18.77        25.45        47.08        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        6.77        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5982 
       94.45        10.85        21.76        84.30         2.40        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ 
       67.96        65.65        12.26        22.78        62.63        12.00 
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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
       35.87         2.01        19.43        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       75.55       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
        0.76        19.63        19.73        12.46        16.96         8.48 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
       16.31        15.75         8.28        12.46        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E 
        0.46         1.15        43.99        22.06        17.23        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-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
       13.08         2.40         0.43        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       23.08        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 
       19.99        85.78        88.24        96.69        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09        42.94        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       92.58        52.27        50.60        78.90        47.90        49.45 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C 
       47.47        65.13       110.73        51.35        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.16              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           153.73            194.79 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           27.565            36.675 
[1] "0.2 - 153.7 (27.6)" "0.1 - 194.8 (36.7)"
[1] "hr=" "1.6"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q GAIN MUTATED        27       23        29       22
  8Q GAIN WILD-TYPE     427       80       161       82
D16V3, multiclass
           clus
vv          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                27               427
  STAGE II               23                80
  STAGE III              29               161
  STAGE IV               22                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    28  24  48   3
  8Q GAIN WILD-TYPE 452 103 210  12
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1              28               452
  T2              24               103
  T3              48               210
  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 GAIN MUTATED    42  12   3
  8Q GAIN WILD-TYPE 281  32   3
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              42               281
  N1              12                32
  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"
D16V6, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    57  18
  8Q GAIN WILD-TYPE 489  71
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     57   18
  8Q GAIN WILD-TYPE  489   71
   clus
vv  8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  0              57               489
  1              18                71
[1] 2 2
[1] FALSE
D16V7, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    33  70
  8Q GAIN WILD-TYPE 259 520
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     33   70
  8Q GAIN WILD-TYPE  259  520
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              33               259
  MALE                70               520
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED    42   0
  8Q GAIN WILD-TYPE 366   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     42    0
  8Q GAIN WILD-TYPE  366    3
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO               42               366
  YES               0                 3
[1] 2 2
[1] FALSE
D16V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8Q GAIN MUTATED                   17                                61
  8Q GAIN WILD-TYPE                 49                               467
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8Q GAIN MUTATED                                      25
  8Q GAIN WILD-TYPE                                   263
D16V10, multiclass
                                       clus
vv                                      8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                 17                49
  KIDNEY CLEAR CELL RENAL CARCINOMA                  61               467
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              25               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"
D16V11, continuous
D16V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q GAIN MUTATED                                  0     3
  8Q GAIN WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED                           8    90
  8Q GAIN WILD-TYPE                       113   629
D16V13, multiclass
                                  clus
vv                                 8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                      8               113
  WHITE                                         90               629
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V14, binary
                   cls
clus                  0   1
  8Q GAIN MUTATED     4  68
  8Q GAIN WILD-TYPE  38 554
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      4   68
  8Q GAIN WILD-TYPE   38  554
                        clus
vv                       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   4                38
  NOT HISPANIC OR LATINO              68               554
[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 628 222
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               26               850 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                6               222 
$`9P GAIN MUTATED`
TCGA-BP-4331 TCGA-BP-5181 TCGA-BQ-7058 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 
       80.68        49.15        11.28       137.06        98.96        24.79 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 
      151.96        49.97        52.27       100.47       104.55       105.60 
TCGA-A3-3374 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4698 TCGA-BP-4770 
       43.20       109.41       112.08        94.19         1.38        10.82 
TCGA-BP-4969 TCGA-CJ-4870 TCGA-CJ-4884 TCGA-CJ-4897 TCGA-CZ-4866 TCGA-CZ-5457 
       58.98        49.25        57.83       109.84       107.41        90.54 
TCGA-B3-4104 TCGA-GL-7966 
       34.49         3.68 

$`9P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4342 
       15.42       111.02        94.72        32.61         3.58        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       48.10        62.86        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-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-KL-8346 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 
       28.80        54.74        62.37        44.91       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         3.55         0.99        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8410 
      105.47        10.68       103.40        92.71        16.67       103.10 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       99.88        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      117.80       122.56        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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-B0-4699 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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        13.15        61.68         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-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       116.84        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 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       50.01        24.66        39.45        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       93.04        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       29.03        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.38              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           151.96            194.79 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            69.83             34.34 
[1] "1.4 - 152.0 (69.8)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.8"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P GAIN MUTATED         7        9         7        3
  9P GAIN WILD-TYPE     447       94       183      101
D17V3, multiclass
           clus
vv          9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                 7               447
  STAGE II                9                94
  STAGE III               7               183
  STAGE IV                3               101
[1] 4 2
[1] TRUE
[1] "dimension of 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   8   2
  9P GAIN WILD-TYPE 473 118 250  13
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               7               473
  T2               9               118
  T3               8               250
  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
  9P GAIN MUTATED    13   1   1
  9P GAIN WILD-TYPE 310  43   5
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              13               310
  N1               1                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"
D17V6, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    22   0
  9P GAIN WILD-TYPE 524  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     22    0
  9P GAIN WILD-TYPE  524   89
   clus
vv  9P GAIN MUTATED 9P GAIN WILD-TYPE
  0              22               524
  1               0                89
[1] 2 2
[1] FALSE
D17V7, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    15  11
  9P GAIN WILD-TYPE 277 579
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15   11
  9P GAIN WILD-TYPE  277  579
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              15               277
  MALE                11               579
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    13   0
  9P GAIN WILD-TYPE 395   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     13    0
  9P GAIN WILD-TYPE  395    3
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO               13               395
  YES               0                 3
[1] 2 2
[1] FALSE
D17V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9P GAIN MUTATED                    9                                14
  9P GAIN WILD-TYPE                 57                               514
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9P GAIN MUTATED                                       3
  9P GAIN WILD-TYPE                                   285
D17V10, multiclass
                                       clus
vv                                      9P GAIN MUTATED 9P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  14               514
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               3               285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
D17V12, continuous
[1] "Remove cluster labels:" "9P GAIN MUTATED"       
clus
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                2                72 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-2Z-A9JD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-A3-A8OV 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451        TCGA-B2-A4SR 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5550        TCGA-MM-A563        TCGA-T7-A92I 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4117 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6793 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" "9P GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        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" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P GAIN MUTATED                                  0     1
  9P GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED                           2    23
  9P GAIN WILD-TYPE                       119   696
D17V13, multiclass
                                  clus
vv                                 9P GAIN MUTATED 9P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      2               119
  WHITE                                         23               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"
D17V14, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     2  19
  9P GAIN WILD-TYPE  40 603
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      2   19
  9P GAIN WILD-TYPE   40  603
                        clus
vv                       9P GAIN MUTATED 9P GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              19               603
[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 631 221
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               24               852 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                7               221 
$`9Q GAIN MUTATED`
TCGA-BQ-7058 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8443 
       11.28       137.06        98.96        24.79       151.96        49.97 
TCGA-KN-8428 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8414 TCGA-A3-3374 TCGA-AK-3429 
       52.27       100.47       104.55       105.60        43.20       109.41 
TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4698 TCGA-BP-4770 TCGA-BP-4969 
      112.08        94.19         3.32         1.38        10.82        58.98 
TCGA-CJ-4884 TCGA-CJ-4897 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5468 TCGA-GL-7966 
       57.83       109.84       107.41        90.54         1.94         3.68 

$`9Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       26.27        20.12        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 
       23.84       109.22        90.48       108.62        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 
       73.91        71.41        28.80        54.74        62.37        44.91 
TCGA-KM-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-8406 TCGA-KO-8407 
       42.35       100.87       105.47        10.68       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       103.10        99.88        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
       10.62        29.10       117.80       122.56        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61       109.51        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4699 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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        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-4343 
       15.62         0.07        93.99        18.48        52.24        62.86 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-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-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       31.30        36.95         3.88        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        61.91       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       63.98       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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 
            74.76             34.90 
[1] "1.4 - 152.0 (74.8)" "0.1 - 194.8 (34.9)"
[1] "hr=" "1.3"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q GAIN MUTATED         5        8         6        5
  9Q GAIN WILD-TYPE     449       95       184       99
D18V3, multiclass
           clus
vv          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                 5               449
  STAGE II                8                95
  STAGE III               6               184
  STAGE IV                5                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
  9Q GAIN MUTATED     5   8   8   3
  9Q GAIN WILD-TYPE 475 119 250  12
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               5               475
  T2               8               119
  T3               8               250
  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   1
  9Q GAIN WILD-TYPE 310  43   5
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              13               310
  N1               1                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"
D18V6, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    18   2
  9Q GAIN WILD-TYPE 528  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     18    2
  9Q GAIN WILD-TYPE  528   87
   clus
vv  9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  0              18               528
  1               2                87
[1] 2 2
[1] FALSE
D18V7, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    13  11
  9Q GAIN WILD-TYPE 279 579
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13   11
  9Q GAIN WILD-TYPE  279  579
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              13               279
  MALE                11               579
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    13   0
  9Q GAIN WILD-TYPE 395   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13    0
  9Q GAIN WILD-TYPE  395    3
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO               13               395
  YES               0                 3
[1] 2 2
[1] FALSE
D18V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9Q GAIN MUTATED                    9                                13
  9Q GAIN WILD-TYPE                 57                               515
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9Q GAIN MUTATED                                       2
  9Q GAIN WILD-TYPE                                   286
D18V10, multiclass
                                       clus
vv                                      9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  13               515
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               2               286
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
D18V12, continuous
[1] "Remove cluster labels:" "9Q GAIN MUTATED"       
clus
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                2                72 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-2Z-A9JD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8345 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408        TCGA-A3-A8OV 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451        TCGA-B2-A4SR 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5550        TCGA-MM-A563        TCGA-T7-A92I 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W        TCGA-4A-A93Y 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0        TCGA-AL-3472 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114        TCGA-B9-4117 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6793 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB        TCGA-G7-A8LD 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD        TCGA-HE-A5NI 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856        TCGA-P4-A5E6 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S        TCGA-SX-A71U 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR        TCGA-SX-A7SS 
"9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" "9Q GAIN WILD-TYPE" 
       TCGA-UZ-A9PM        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" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q GAIN MUTATED                                  0     1
  9Q GAIN WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED                           1    22
  9Q GAIN WILD-TYPE                       120   697
D18V13, multiclass
                                  clus
vv                                 9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      1               120
  WHITE                                         22               697
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V14, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     2  18
  9Q GAIN WILD-TYPE  40 604
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      2   18
  9Q GAIN WILD-TYPE   40  604
                        clus
vv                       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              18               604
[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 627 221
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                28                848 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                221 
$`10P GAIN MUTATED`
TCGA-CZ-4854 TCGA-AL-3468 TCGA-KL-8324 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8436 
       46.16        76.64       153.73         0.99        11.21        42.35 
TCGA-A3-3316 TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 
       49.08        83.21         1.41        19.30         5.10         5.46 
TCGA-BP-4338 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 TCGA-CZ-4858 
       93.99        13.15        68.38        30.64        66.31        69.21 
TCGA-CZ-4866 TCGA-CZ-5454 TCGA-EU-5905 TCGA-5P-A9K9 TCGA-A4-8098 TCGA-B9-4617 
      107.41        23.74         3.91        19.36        29.46         1.15 
TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-HE-7130 TCGA-SX-A7SS 
       13.08         1.18        58.19        53.10 

$`10P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        12.99        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         3.55        52.27        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       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       36.82         0.53        39.16        24.16        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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80       122.56       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61       109.51        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       40.01        94.29        37.58        38.40        82.45        72.89 
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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        58.59        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         5.75         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
       10.82         5.33        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
        2.04        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-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
       58.75         6.77        14.66        63.39        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       84.30        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
       62.63        53.46        12.00        18.12         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       16.37        11.70         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       43.04        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       16.64        30.48        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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         0.46        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       74.60        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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.99               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            153.73             194.79 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            30.050             35.915 
[1] "1.0 - 153.7 (30.1)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1"  
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P GAIN MUTATED        11        6         4        5
  10P GAIN WILD-TYPE     443       97       186       99
D19V3, multiclass
           clus
vv          10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                 11                443
  STAGE II                 6                 97
  STAGE III                4                186
  STAGE IV                 5                 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
  10P GAIN MUTATED    12   7   6   3
  10P GAIN WILD-TYPE 468 120 252  12
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1               12                468
  T2                7                120
  T3                6                252
  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     7   4   1
  10P GAIN WILD-TYPE 316  40   5
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                7                316
  N1                4                 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"
D19V6, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    20   3
  10P GAIN WILD-TYPE 526  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     20    3
  10P GAIN WILD-TYPE  526   86
   clus
vv  10P GAIN MUTATED 10P GAIN WILD-TYPE
  0               20                526
  1                3                 86
[1] 2 2
[1] FALSE
D19V7, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    11  17
  10P GAIN WILD-TYPE 281 573
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     11   17
  10P GAIN WILD-TYPE  281  573
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE               11                281
  MALE                 17                573
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 396   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  396    3
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                12                396
  YES                0                  3
[1] 2 2
[1] FALSE
D19V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10P GAIN MUTATED                    4                                16
  10P GAIN WILD-TYPE                 62                               512
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10P GAIN MUTATED                                       8
  10P GAIN WILD-TYPE                                   280
D19V10, multiclass
                                       clus
vv                                      10P GAIN MUTATED 10P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                   16                512
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                8                280
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
D19V12, continuous
[1] "Remove cluster labels:" "10P GAIN MUTATED"      
clus
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 72 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5550         TCGA-MM-A563 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-T7-A92I         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117         TCGA-B9-A69E 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6793 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LB 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-UZ-A9PM         TCGA-UZ-A9PS 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" "10P GAIN WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"10P GAIN WILD-TYPE" "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    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED                           2    23
  10P GAIN WILD-TYPE                       119   696
D19V13, multiclass
                                  clus
vv                                 10P GAIN MUTATED 10P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                       2                119
  WHITE                                          23                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"
D19V14, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     0  19
  10P GAIN WILD-TYPE  42 603
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      0   19
  10P GAIN WILD-TYPE   42  603
                        clus
vv                       10P GAIN MUTATED 10P GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               19                603
[1] 2 2
[1] FALSE

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED    15   7
  10Q GAIN WILD-TYPE 633 221
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                22                854 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                221 
$`10Q GAIN MUTATED`
TCGA-CZ-4854 TCGA-AL-3468 TCGA-KL-8324 TCGA-KN-8427 TCGA-AK-3453 TCGA-B0-5109 
       46.16        76.64       153.73         0.99        83.21        19.30 
TCGA-B4-5832 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-5175 TCGA-CW-5588 
        5.10        11.31        13.15        68.38        30.64        66.31 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-EU-5905 TCGA-5P-A9K9 TCGA-A4-8098 
       69.21       107.41        23.74         3.91        19.36        29.46 
TCGA-B9-4617 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-SX-A7SS 
        1.15        13.08         1.18        53.10 

$`10Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        12.99        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         3.55        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 
       46.78        48.36        78.64        40.01        94.29        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        2.14        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       58.59        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         5.75         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       61.78        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       74.20        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 
      105.93        83.90        18.77        25.45        47.08        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        6.77        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       53.46        12.00        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       26.40        20.61         0.46        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A97G 
       34.19        19.00        24.89        10.68         2.40         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              0.99               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
            153.73             194.79 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              26.6               36.0 
[1] "1.0 - 153.7 (26.6)" "0.1 - 194.8 (36.0)"
[1] "hr=" "1.4"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q GAIN MUTATED        10        4         2        4
  10Q GAIN WILD-TYPE     444       99       188      100
D20V3, multiclass
           clus
vv          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                 10                444
  STAGE II                 4                 99
  STAGE III                2                188
  STAGE IV                 4                100
[1] 4 2
[1] TRUE
[1] "dimension of 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 469 122 254  13
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1               11                469
  T2                5                122
  T3                4                254
  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     6   3   1
  10Q GAIN WILD-TYPE 317  41   5
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                6                317
  N1                3                 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"
D20V6, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    16   3
  10Q GAIN WILD-TYPE 530  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     16    3
  10Q GAIN WILD-TYPE  530   86
   clus
vv  10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  0               16                530
  1                3                 86
[1] 2 2
[1] FALSE
D20V7, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED    10  12
  10Q GAIN WILD-TYPE 282 578
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED     10   12
  10Q GAIN WILD-TYPE  282  578
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE               10                282
  MALE                 12                578
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     8   0
  10Q GAIN WILD-TYPE 400   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      8    0
  10Q GAIN WILD-TYPE  400    3
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 8                400
  YES                0                  3
[1] 2 2
[1] FALSE
D20V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10Q GAIN MUTATED                    2                                13
  10Q GAIN WILD-TYPE                 64                               515
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10Q GAIN MUTATED                                       7
  10Q GAIN WILD-TYPE                                   281
D20V10, multiclass
                                       clus
vv                                      10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   13                515
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                7                281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 2                104 
        TCGA-B8-4621         TCGA-DV-A4W0         TCGA-G6-A8L7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-KL-8330         TCGA-KL-8335 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8433         TCGA-KO-8408 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416         TCGA-A3-A8CQ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-4146 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-5550 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-G6-A5PC 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J2 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"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-4A-A93W 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9K3         TCGA-5P-A9KE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-A48D         TCGA-A4-A57E 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3466         TCGA-AL-3472 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"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-HE-A5NJ         TCGA-HE-A5NK 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IA-A83V 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-P4-A5EB         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-A9PS 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-Y8-A894 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A896         TCGA-Y8-A8RY 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
D20V12, continuous
[1] "Remove cluster labels:" "10Q GAIN MUTATED"      
clus
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 73 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-B8-5550 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J3 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LD         TCGA-G7-A8LE 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-GL-7773         TCGA-GL-A9DD         TCGA-HE-A5NI 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-IA-A40U         TCGA-MH-A854         TCGA-MH-A856 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-P4-A5E6         TCGA-P4-AAVK         TCGA-Q2-A5QZ 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A7SL 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SR         TCGA-UZ-A9PM 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" "10Q GAIN WILD-TYPE" 
        TCGA-Y8-A8RY 
"10Q GAIN WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q GAIN MUTATED                                  0     2
  10Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED                           2    18
  10Q GAIN WILD-TYPE                       119   701
D20V13, multiclass
                                  clus
vv                                 10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                       2                119
  WHITE                                          18                701
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V14, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     0  16
  10Q GAIN WILD-TYPE  42 606
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      0   16
  10Q GAIN WILD-TYPE   42  606
                        clus
vv                       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               16                606
[1] 2 2
[1] FALSE

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED    41  15
  11P GAIN WILD-TYPE 607 213
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                56                820 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                15                213 
$`11P GAIN MUTATED`
TCGA-KL-8339 TCGA-BP-4799 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5892 TCGA-KL-8324 
       28.11        37.25        49.25        11.87        11.97       153.73 
TCGA-KL-8341 TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8433 
       24.79       151.96        23.47        25.91       104.52        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      100.47       104.55       103.10        99.88       105.60        96.62 
TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 
       24.16        24.16       112.08        94.19        83.21        57.70 
TCGA-B0-4844 TCGA-B0-5113 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 
       10.29        38.63         5.10        25.55         4.93        89.36 
TCGA-BP-4337 TCGA-BP-4351 TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 
        0.07        31.89        43.00        37.22        34.95        46.55 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4885 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5682 
       11.05        79.66       113.46        49.28        22.32       122.83 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 TCGA-EU-5905 
       69.21         6.77       107.41        94.45         1.94         3.91 
TCGA-A4-A57E TCGA-B9-4117 TCGA-BQ-5889 TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 
        8.48         0.46        10.82        13.08        23.08         3.68 
TCGA-P4-A5EA TCGA-P4-A5EB 
        6.61        99.12 

$`11P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       20.38         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        12.99        76.64        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       10.16        21.86        19.23        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
       38.07        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.56        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       54.74        62.37        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8426 
       31.33       129.37        87.91        25.48        65.19         3.55 
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-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87       105.47        10.68       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       92.71        16.67        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 
       46.78        48.36        78.64        40.01        94.29        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        2.14         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        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-B0-5092 TCGA-B0-5094 
       11.24        11.90         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.75         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       45.37        17.19        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        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-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
       27.78        62.07        37.25        21.21        15.62        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
        3.88        46.45        16.47        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       38.30        42.44        37.25        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        19.82         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       58.95        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       47.67        49.97        51.29        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       72.00       129.40       133.71        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
       18.15        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 
      105.93        83.90        18.77        25.45        47.08        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        2.40        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
       20.61         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        30.28        25.35         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-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        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       20.52        25.84        25.25        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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED 
       31.13        15.48        99.78        87.09        42.94        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.07               0.10 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            153.73             194.79 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            36.085             35.900 
[1] "0.1 - 153.7 (36.1)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1.1"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P GAIN MUTATED        18        9        18       12
  11P GAIN WILD-TYPE     436       94       172       92
D21V3, multiclass
           clus
vv          11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                 18                436
  STAGE II                 9                 94
  STAGE III               18                172
  STAGE IV                12                 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
  11P GAIN MUTATED    18  11  28   1
  11P GAIN WILD-TYPE 462 116 230  14
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1               18                462
  T2               11                116
  T3               28                230
  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 300  39   5
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               23                300
  N1                5                 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"
D21V6, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    32  11
  11P GAIN WILD-TYPE 514  78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     32   11
  11P GAIN WILD-TYPE  514   78
   clus
vv  11P GAIN MUTATED 11P GAIN WILD-TYPE
  0               32                514
  1               11                 78
[1] 2 2
[1] FALSE
D21V7, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    21  37
  11P GAIN WILD-TYPE 271 553
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     21   37
  11P GAIN WILD-TYPE  271  553
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               21                271
  MALE                 37                553
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    30   1
  11P GAIN WILD-TYPE 378   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     30    1
  11P GAIN WILD-TYPE  378    2
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                30                378
  YES                1                  2
[1] 2 2
[1] FALSE
D21V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11P GAIN MUTATED                   15                                31
  11P GAIN WILD-TYPE                 51                               497
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11P GAIN MUTATED                                      12
  11P GAIN WILD-TYPE                                   276
D21V10, multiclass
                                       clus
vv                                      11P GAIN MUTATED 11P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  15                 51
  KIDNEY CLEAR CELL RENAL CARCINOMA                   31                497
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               12                276
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
D21V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P GAIN MUTATED                                  0     2
  11P GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED                           5    51
  11P GAIN WILD-TYPE                       116   668
D21V13, multiclass
                                  clus
vv                                 11P GAIN MUTATED 11P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                       5                116
  WHITE                                          51                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"
D21V14, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     4  39
  11P GAIN WILD-TYPE  38 583
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      4   39
  11P GAIN WILD-TYPE   38  583
                        clus
vv                       11P GAIN MUTATED 11P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               39                583
[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 606 216
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                54                822 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                12                216 
$`11Q GAIN MUTATED`
TCGA-KL-8339 TCGA-BP-4799 TCGA-AL-A5DJ TCGA-BQ-5892 TCGA-KL-8324 TCGA-KL-8341 
       28.11        37.25        49.25        11.97       153.73        24.79 
TCGA-KM-8438 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 
      151.96        23.47        25.91       104.52         3.55        11.21 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      100.47       104.55       103.10        99.88       105.60        96.62 
TCGA-A3-3313 TCGA-A3-3372 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4710 
       24.16        24.16       112.08        94.19        83.21        57.70 
TCGA-B0-4844 TCGA-B0-5113 TCGA-B2-4099 TCGA-B8-4620 TCGA-B8-A54I TCGA-BP-4167 
       10.29        38.63        31.96        25.55         4.93        89.36 
TCGA-BP-4337 TCGA-BP-4351 TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5200 TCGA-CJ-4635 
        0.07        31.89        43.00        37.22        34.95        46.55 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4885 TCGA-CJ-4907 TCGA-CJ-5679 TCGA-CJ-5682 
       11.05        79.66       113.46        49.28        22.32       122.83 
TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-EU-5905 TCGA-A4-A57E TCGA-B9-4117 
       69.21       107.41        94.45         3.91         8.48         0.46 
TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-GL-7966 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-Q2-A5QZ 
       13.08        23.08         3.68         6.61        99.12        14.07 

$`11Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       20.38         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
        0.89        12.99        76.64        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
        6.74        38.07        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-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-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        54.74        62.37        44.91        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-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-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 
      115.00        42.35       100.87       105.47        10.68       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       92.71        16.67        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 
       46.78        48.36        78.64        40.01        94.29        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        2.14         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        10.52        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-B0-5092 TCGA-B0-5094 
       11.24        11.90         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 
       91.46        32.61        35.90         1.68        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       45.37        17.19        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        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-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
       27.78        62.07        37.25        21.21        15.62        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       14.93        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
        3.88        46.45        16.47        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       38.30        42.44        37.25        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        19.82         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       58.95        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       47.67        49.97        51.29        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       72.00       129.40       133.71        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
       18.15        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 
      105.93        83.90        18.77        25.45        47.08        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        6.77        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       55.33        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       53.46        12.00        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP TCGA-AL-3466 
       16.96        16.31        15.75         8.28        12.46         9.63 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       28.18        26.40        20.61         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       74.60        34.19        19.00        24.89        10.68         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09        42.94        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.07               0.10 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            153.73             194.79 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            37.235             35.885 
[1] "0.1 - 153.7 (37.2)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1.4"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q GAIN MUTATED        19        9        16       10
  11Q GAIN WILD-TYPE     435       94       174       94
D22V3, multiclass
           clus
vv          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                 19                435
  STAGE II                 9                 94
  STAGE III               16                174
  STAGE IV                10                 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
  11Q GAIN MUTATED    19  11  25   0
  11Q GAIN WILD-TYPE 461 116 233  15
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1               19                461
  T2               11                116
  T3               25                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
  11Q GAIN MUTATED    22   3   1
  11Q GAIN WILD-TYPE 301  41   5
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               22                301
  N1                3                 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"
D22V6, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    32   9
  11Q GAIN WILD-TYPE 514  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     32    9
  11Q GAIN WILD-TYPE  514   80
   clus
vv  11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  0               32                514
  1                9                 80
[1] 2 2
[1] FALSE
D22V7, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    22  33
  11Q GAIN WILD-TYPE 270 557
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     22   33
  11Q GAIN WILD-TYPE  270  557
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               22                270
  MALE                 33                557
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    31   1
  11Q GAIN WILD-TYPE 377   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     31    1
  11Q GAIN WILD-TYPE  377    2
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                31                377
  YES                1                  2
[1] 2 2
[1] FALSE
D22V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11Q GAIN MUTATED                   16                                29
  11Q GAIN WILD-TYPE                 50                               499
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11Q GAIN MUTATED                                      10
  11Q GAIN WILD-TYPE                                   278
D22V10, multiclass
                                       clus
vv                                      11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  16                 50
  KIDNEY CLEAR CELL RENAL CARCINOMA                   29                499
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               10                278
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
D22V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q GAIN MUTATED                                  0     2
  11Q GAIN WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED                           5    48
  11Q GAIN WILD-TYPE                       116   671
D22V13, multiclass
                                  clus
vv                                 11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                       5                116
  WHITE                                          48                671
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V14, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     4  36
  11Q GAIN WILD-TYPE  38 586
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      4   36
  11Q GAIN WILD-TYPE   38  586
                        clus
vv                       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               36                586
[1] 2 2
[1] FALSE

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                  0   1
  12P GAIN MUTATED   179  69
  12P GAIN WILD-TYPE 469 159
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
               248                628 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                69                159 
$`12P GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 
       28.11        38.47        42.97       109.91        19.73        43.96 
TCGA-B0-4815 TCGA-B8-4621 TCGA-BP-4782 TCGA-BP-4988 TCGA-BP-5009 TCGA-BP-5178 
       52.21        25.91        11.64        27.22        35.90        62.86 
TCGA-BP-5191 TCGA-CJ-4636 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-2Z-A9JL TCGA-2Z-A9JT 
       31.79        63.25        46.16         0.59        33.07        22.49 
TCGA-A4-7584 TCGA-AL-3468 TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-DW-5561 
       21.37        76.64        10.16        19.23        11.97        13.61 
TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
       37.55         3.75        14.63        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-KL-8324 TCGA-KL-8327 
       67.17        19.73        17.75        62.83       153.73       137.06 
TCGA-KL-8331 TCGA-KL-8343 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
       98.96        71.41        62.37       151.96        49.97        23.47 
TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8436 TCGA-KO-8409 
       25.91         3.55         0.99        52.27        42.35       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-A3-3311 TCGA-A3-3319 TCGA-A3-3347 
      103.10        99.88       105.60        39.16        37.15        52.93 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI TCGA-AK-3430 
       24.16        43.20        18.87        20.28        33.47        15.78 
TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 
      112.08       109.51        94.19        83.21         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4713 
        4.57         2.53         1.38         3.62        57.70         6.64 
TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 
       46.59         6.02        40.44        36.53        14.93        10.09 
TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5075 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 
       27.42        29.03        20.94        11.90         7.30        10.95 
TCGA-B0-5095 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 
        8.05        30.48        19.30        38.63        41.88        85.78 
TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4622 
       86.47        91.46         5.10         5.46        23.31        50.14 
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-4787 TCGA-BP-4803 TCGA-BP-4804 
       11.31         5.98        13.15        15.78         6.71        47.97 
TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 
       71.41        60.30        61.22        14.93        46.45        31.30 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5194 
       16.47        43.00         2.04        30.64        37.22        13.41 
TCGA-BP-5200 TCGA-CJ-4638 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4884 TCGA-CJ-4903 
       34.95        14.17        47.18        74.27        57.83        51.29 
TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 
       49.28        54.48         4.57        18.81       131.08       133.71 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 
       22.32       122.83        73.35        53.42        66.31        74.66 
TCGA-CW-6087 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 
        1.35        47.08       107.41        79.63        10.85        69.96 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-A4VX 
       22.52         1.94        31.10        67.96        14.63        53.46 
TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        3.91         7.04        75.55        59.01       100.27        56.91 
TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-5P-A9K0 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       54.64        30.71        22.26        19.36        12.99        12.39 
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-3471 TCGA-AL-7173 TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B9-4113 
       49.32        67.73        36.49        20.32        33.83        50.50 
TCGA-B9-4114 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH 
       28.18         1.15        43.99        22.06         0.16        17.49 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-7059 
        8.88        43.20        25.35        10.82         0.95         7.63 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-F9-A7Q0 
        7.17         3.81        40.77        80.88        51.19        13.08 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1.18         4.01        39.25        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       16.90       194.79         3.68         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-HE-7130 TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
       11.21        58.19        11.84        56.75        25.22        16.80 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
        2.04        85.78        88.24        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB 
       34.29        27.78        30.38        20.25        17.62        99.12 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ 
       52.27        16.01        44.61        28.80        11.93        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-UZ-A9Q1 
       26.47        53.10       103.63        98.96        65.13        51.35 
TCGA-V9-A7HT TCGA-Y8-A8RY 
       31.73        25.28 

$`12P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       34.29        31.07        82.32        58.49        28.73        22.45 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
      126.05        24.82         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 
       12.33        77.62        44.15        60.59        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4993 TCGA-BP-4995 
        6.94        61.51        53.65        25.81         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 
       41.62        27.62        48.10        49.15        27.02        44.55 
TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       31.27       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      118.85        75.58       103.43       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-5P-A9JU TCGA-5P-A9JV 
       34.85        39.88        25.58        16.18        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       61.05         0.89        12.99        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.07        21.86        11.87        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        48.85       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-IZ-A6M8 TCGA-MH-A855 
       35.93        24.46        13.78         3.02        16.34        12.13 
TCGA-MH-A857 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       29.26        41.33        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
        6.74        38.07        23.84       109.22        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-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       44.91       123.12        51.06        31.33       129.37        87.91 
TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19       104.52        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       11.21        59.08       115.00       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8415 TCGA-KO-8416 
      100.47       103.40        92.71        16.67        96.62        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3313 
       92.55        12.66        11.90        36.82         0.53        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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01         4.50        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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       117.80       122.56       109.41        73.68 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       68.61        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-AS-3778 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 
        1.41         3.48        28.47        19.00        65.10         7.82 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        5.98         2.14         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 
        5.52        45.07        33.50        16.77        54.48        29.10 
TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4839 TCGA-B0-4841 
       78.44        68.71        40.70        45.30        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 
        2.27        36.85        70.52        43.30        11.24        25.32 
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        58.59        66.05        52.73 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       42.41       111.52       129.67       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       89.49        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       25.55        40.04        23.74         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60         6.38        48.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       29.88         1.74        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       90.28        99.85         0.43        23.05        77.03        62.24 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       21.21        15.62        18.48        52.24        62.86        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-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       77.98        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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4959 
       48.95        36.53        36.39        10.98        36.95        87.45 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       63.62        58.68         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-4981 
       48.89        49.38        45.50         6.94        47.11        36.07 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5000 
       33.34        36.95         3.88        46.45        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       79.30        74.20        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       24.62        33.47        19.82         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       73.22       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        79.66        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-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 
      129.40        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       67.00        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
       81.83         5.39        85.78        73.18        78.18       105.93 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       83.90        18.77        25.45        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       10.22        21.76        84.30         2.40        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 
       65.65        12.26        22.78        62.63        12.00        18.12 
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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J3 TCGA-2Z-A9J7 
       19.43        19.96        16.37        11.70        58.22         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        51.52        38.99        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       43.04        27.09        67.43        19.63         0.10        35.18 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
        7.82         0.23        16.64        23.97        23.28        23.31 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 
       14.33        12.46         8.48         8.28         9.63        70.19 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 
       66.71        62.66         2.20        41.13        37.51        20.25 
TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
       16.77        29.03        30.58        34.49        12.46        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.61         0.46        17.23        14.86        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       19.27        63.72        22.92        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        30.28         7.66         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 
       48.26        93.34        61.28        50.40        49.84         7.04 
TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       79.86        74.60        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        90.90        11.05        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
       25.15        20.52        25.84        80.65        12.92        27.65 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83V 
       16.31        81.93        26.01        73.25        19.99        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       27.65        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
        6.61        92.58        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SU TCGA-UN-AAZ9 
       49.45        27.06        19.00        16.31        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS 
       26.20       117.40       125.29        37.35        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       30.67        47.47       110.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05         6.02        13.28 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.07               0.10 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            194.79             149.16 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            29.065             37.495 
[1] "0.1 - 194.8 (29.1)" "0.1 - 149.2 (37.5)"
[1] "hr=" "1.3"
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P GAIN MUTATED       118       27        54       41
  12P GAIN WILD-TYPE     336       76       136       63
D23V3, multiclass
           clus
vv          12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                118                336
  STAGE II                27                 76
  STAGE III               54                136
  STAGE IV                41                 63
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  12P GAIN MUTATED   126  34  83   7
  12P GAIN WILD-TYPE 354  93 175   8
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1              126                354
  T2               34                 93
  T3               83                175
  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    87  21   3
  12P GAIN WILD-TYPE 236  23   3
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               87                236
  N1               21                 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"
D23V6, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   129  33
  12P GAIN WILD-TYPE 417  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    129   33
  12P GAIN WILD-TYPE  417   56
   clus
vv  12P GAIN MUTATED 12P GAIN WILD-TYPE
  0              129                417
  1               33                 56
[1] 2 2
[1] FALSE
D23V7, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    66 186
  12P GAIN WILD-TYPE 226 404
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     66  186
  12P GAIN WILD-TYPE  226  404
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               66                226
  MALE                186                404
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED   121   1
  12P GAIN WILD-TYPE 287   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED    121    1
  12P GAIN WILD-TYPE  287    2
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO               121                287
  YES                1                  2
[1] 2 2
[1] FALSE
D23V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12P GAIN MUTATED                   19                               121
  12P GAIN WILD-TYPE                 47                               407
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12P GAIN MUTATED                                     112
  12P GAIN WILD-TYPE                                   176
D23V10, multiclass
                                       clus
vv                                      12P GAIN MUTATED 12P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  19                 47
  KIDNEY CLEAR CELL RENAL CARCINOMA                  121                407
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              112                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"
D23V11, continuous
D23V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12P GAIN MUTATED                                  0     4
  12P GAIN WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED                          32   207
  12P GAIN WILD-TYPE                        89   512
D23V13, multiclass
                                  clus
vv                                 12P GAIN MUTATED 12P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                 12
  BLACK OR AFRICAN AMERICAN                      32                 89
  WHITE                                         207                512
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V14, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     7 190
  12P GAIN WILD-TYPE  35 432
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      7  190
  12P GAIN WILD-TYPE   35  432
                        clus
vv                       12P GAIN MUTATED 12P GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 35
  NOT HISPANIC OR LATINO              190                432
[1] 2 2
[1] FALSE

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                  0   1
  12Q GAIN MUTATED   181  71
  12Q GAIN WILD-TYPE 467 157
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
               252                624 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                71                157 
$`12Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3358 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 
       28.11        38.47        42.97       109.91        19.73        43.96 
TCGA-B0-4815 TCGA-B8-4621 TCGA-BP-4782 TCGA-BP-4988 TCGA-BP-5009 TCGA-BP-5178 
       52.21        25.91        11.64        27.22        35.90        62.86 
TCGA-BP-5191 TCGA-CJ-4636 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-2Z-A9JL TCGA-2Z-A9JT 
       31.79        63.25        46.16         0.59        33.07        22.49 
TCGA-A4-7584 TCGA-AL-3468 TCGA-B3-A6W5 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-DW-5561 
       21.37        76.64        10.16        19.23        11.97        13.61 
TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
       37.55         3.75        14.63        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-KL-8324 TCGA-KL-8327 
       67.17        19.73        17.75        62.83       153.73       137.06 
TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
       98.96        24.79        71.41        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-KN-8436 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-A3-3311 
       42.35       104.55       103.10        99.88       105.60        39.16 
TCGA-A3-3319 TCGA-A3-3347 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3387 
       37.15        52.93        24.16        43.20        18.87        20.28 
TCGA-A3-A6NI TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 
       33.47        15.78       112.08       109.51        94.19        83.21 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4698 
        3.32         1.41         4.57         2.53        28.47         1.38 
TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4821 
        3.62        57.70         6.64        46.59         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4828 TCGA-B0-4838 TCGA-B0-4848 TCGA-B0-5075 
       36.53        14.93        10.09        27.42        29.03        20.94 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5107 TCGA-B0-5109 
       11.90         7.30        10.95         8.05        30.48        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5713 TCGA-B4-5832 
       38.63        41.88        85.78        86.47        91.46         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4622 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54F 
        5.46        23.31        50.14        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-4787 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4963 TCGA-BP-4964 
       15.78         6.71        47.97        71.41        60.30        61.22 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5173 
       14.93        46.45        31.30        16.47        43.00         2.04 
TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5194 TCGA-BP-5200 TCGA-CJ-4638 TCGA-CJ-4872 
       30.64        37.22        13.41        34.95        14.17        47.18 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 
       74.27        66.21        57.83        51.29        49.28        54.48 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 
        4.57        18.81       131.08       133.71        22.32       122.83 
TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4857 
       73.35        53.42        66.31        74.66         1.35        47.08 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
      107.41        79.63        10.85        69.96        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-A4VX TCGA-EU-5905 TCGA-2K-A9WE 
       31.10        67.96        14.63        53.46         3.91         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JG TCGA-2Z-A9JM 
       75.55        59.01       100.27        56.91        54.64        30.71 
TCGA-5P-A9K0 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-A4-7286 TCGA-A4-7732 
       22.26        19.36        12.99        12.39        18.21        19.13 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
       30.48        29.46        25.64         0.76        19.63        19.73 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3471 TCGA-AL-7173 
       16.96        16.31        15.75        12.46        49.32        67.73 
TCGA-B1-A47N TCGA-B1-A656 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4617 
       36.49        20.32        33.83        50.50        28.18         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5880 
       43.99        22.06         0.16        17.49         8.88        43.20 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5891 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 
       25.35        10.82         0.95         7.63         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 
       40.77        80.88        51.19        13.08         1.18         4.01 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 
       39.25        25.25        17.98        23.08        16.90       194.79 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7130 
        3.68         1.05        12.43        12.89        11.21        58.19 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S 
       11.84        56.75        25.22        16.80         2.04        85.78 
TCGA-IA-A83T TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       88.24        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL 
       30.38        20.25        17.62        99.12        52.27        16.01 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       44.61        28.80        11.93        41.62        26.47        53.10 
TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A8RY 
      103.63        98.96        65.13        51.35        31.73        25.28 

$`12Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       34.29        31.07        82.32        58.49        28.73        22.45 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
      126.05        24.82         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 
       12.33        77.62        44.15        60.59        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4993 TCGA-BP-4995 
        6.94        61.51        53.65        25.81         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 
       41.62        27.62        48.10        49.15        27.02        44.55 
TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       31.27       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      118.85        75.58       103.43       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-5P-A9JU TCGA-5P-A9JV 
       34.85        39.88        25.58        16.18        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       61.05         0.89        12.99        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.07        21.86        11.87        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        48.85       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7842 TCGA-IZ-A6M8 TCGA-MH-A855 
       35.93        24.46        13.78         3.02        16.34        12.13 
TCGA-MH-A857 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       29.26        41.33        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
        6.74        38.07        23.84       109.22        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-8440 
       86.56        66.54        73.91        28.80        54.74        44.91 
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-8405 TCGA-KO-8406 
      115.00       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       92.71        16.67        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       11.90        36.82         0.53        24.16        49.08        49.02 
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-A3-3346 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       62.01         4.50        45.53        29.92        18.44        88.37 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
       51.25        10.49        28.70        74.63        74.76        53.29 
TCGA-A3-3376 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-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-3434 TCGA-AK-3443 
      117.80       122.56       109.41        73.68        68.61        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 
       48.36        78.64        40.01        94.29        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4694 
       82.45        72.89        12.13        40.70         1.41         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4714 
       19.00        65.10         7.82         5.98         2.14         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 
       16.77        54.48        29.10        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        10.52        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-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5096 TCGA-B0-5097 
       43.30        11.24        25.32        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 
       58.59        66.05        52.73        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3923 TCGA-B2-3924 
      130.65        79.89       131.15        89.49        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         1.25         0.53 
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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
       25.05        45.37        17.19        25.55        40.04        23.74 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-B8-A54J 
       34.39        14.30        27.29        29.88         1.74        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4166 
       16.27        14.17        85.51        90.28        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       23.05        77.03        62.24        54.90        97.45        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       27.78        62.07        37.25        21.21        15.62        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 
       52.24        62.86        49.08        44.94        12.23        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 
       31.33        12.30        72.59        77.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        68.38        60.95        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4967 
       10.98        36.95        87.45        63.62        58.68         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-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 
        6.94        47.11        36.07        33.34        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       46.45        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       35.21        28.87         6.35        79.30        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
        9.63        74.40        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       13.35        33.24        23.47        24.62        33.47        19.82 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        46.55        73.22       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
       79.66        75.06       116.84        64.27        71.87        61.91 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-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-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
        3.06        72.00       129.40        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       18.15        62.10        67.00        62.66       119.64         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-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4858 
       78.18       105.93        83.90        18.77        25.45        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
       58.75         6.77        14.66        63.39        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5467 
       55.33        94.45        10.22        21.76        84.30         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
       12.69        80.19        65.65        12.26        22.78        62.63 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK 
       58.22         4.57        91.73        56.81        51.52        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K2 TCGA-5P-A9K3 
       11.57       106.55        49.58        90.21        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 
       71.80        62.93        43.04        27.09        67.43        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8311 
        0.10        35.18         7.82         0.23        16.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 
       23.28        23.31        14.33        12.46         8.48         8.28 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AT-A5NU TCGA-B1-5398 
        9.63        70.19        66.71        62.66         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       37.51        20.25        16.77        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A5W8 TCGA-B9-A69E 
       12.46        26.40        20.61         0.46        17.23        14.86 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 
       12.30        86.76        19.27        63.72        22.92        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 TCGA-BQ-5893 
       21.63        40.83        26.04        30.28         7.66         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7060 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       49.84         7.04        79.86        74.60        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        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LE 
       11.05        71.44        25.15        20.52        25.84        80.65 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NK 
       12.92        27.65        16.31        81.93        26.01        73.25 
TCGA-IA-A40X TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       19.99        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       10.55        10.09        27.65        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO 
       87.09        42.94         6.61        92.58        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP 
       14.07        47.90        49.45        27.06        19.00        16.31 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        18.02        26.20       117.40       125.29        37.35 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-WN-A9G9 
       86.27        71.24        30.67        47.47       110.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       39.06        18.64        18.64        18.05         6.02        13.28 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.07               0.10 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            194.79             149.16 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            28.915             37.545 
[1] "0.1 - 194.8 (28.9)" "0.1 - 149.2 (37.5)"
[1] "hr=" "1.3"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q GAIN MUTATED       118       27        57       42
  12Q GAIN WILD-TYPE     336       76       133       62
D24V3, multiclass
           clus
vv          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                118                336
  STAGE II                27                 76
  STAGE III               57                133
  STAGE IV                42                 62
[1] 4 2
[1] TRUE
[1] "dimension of 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   126  34  87   7
  12Q GAIN WILD-TYPE 354  93 171   8
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1              126                354
  T2               34                 93
  T3               87                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
  12Q GAIN MUTATED    88  21   4
  12Q GAIN WILD-TYPE 235  23   2
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               88                235
  N1               21                 23
  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"
D24V6, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   132  33
  12Q GAIN WILD-TYPE 414  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    132   33
  12Q GAIN WILD-TYPE  414   56
   clus
vv  12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  0              132                414
  1               33                 56
[1] 2 2
[1] FALSE
D24V7, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    67 189
  12Q GAIN WILD-TYPE 225 401
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     67  189
  12Q GAIN WILD-TYPE  225  401
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               67                225
  MALE                189                401
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED   123   1
  12Q GAIN WILD-TYPE 285   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED    123    1
  12Q GAIN WILD-TYPE  285    2
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO               123                285
  YES                1                  2
[1] 2 2
[1] FALSE
D24V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12Q GAIN MUTATED                   21                               123
  12Q GAIN WILD-TYPE                 45                               405
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12Q GAIN MUTATED                                     112
  12Q GAIN WILD-TYPE                                   176
D24V10, multiclass
                                       clus
vv                                      12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  123                405
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              112                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"
D24V11, continuous
D24V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q GAIN MUTATED                                  0     5
  12Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED                          32   210
  12Q GAIN WILD-TYPE                        89   509
D24V13, multiclass
                                  clus
vv                                 12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           5                 11
  BLACK OR AFRICAN AMERICAN                      32                 89
  WHITE                                         210                509
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V14, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     7 193
  12Q GAIN WILD-TYPE  35 429
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      7  193
  12Q GAIN WILD-TYPE   35  429
                        clus
vv                       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    7                 35
  NOT HISPANIC OR LATINO              193                429
[1] 2 2
[1] FALSE

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                  0   1
  13Q GAIN MUTATED    44   8
  13Q GAIN WILD-TYPE 604 220
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                52                824 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 8                220 
$`13Q GAIN MUTATED`
TCGA-A3-3325 TCGA-CJ-5689 TCGA-DV-5574 TCGA-A4-A5Y1 TCGA-BQ-7046 TCGA-DW-5561 
       38.47        53.26        66.28        12.99        96.92        13.61 
TCGA-KN-8419 TCGA-KN-8436 TCGA-AK-3453 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5690 
       23.47        42.35        83.21         2.14        57.70       111.52 
TCGA-B2-5639 TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4983 TCGA-BP-5198 TCGA-BP-5200 
       32.98         0.43        37.25        46.45        19.82        34.95 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 
       49.18        49.28        54.48       131.08       133.71       122.83 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-2Z-A9J1 TCGA-4A-A93X TCGA-5P-A9K4 
       94.45        10.85        69.96        75.55        12.82        71.80 
TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B3-8121 
       23.97        19.73        14.33         2.20        41.13        12.46 
TCGA-B9-4117 TCGA-B9-4617 TCGA-BQ-5885 TCGA-DZ-6133 TCGA-EV-5903 TCGA-G7-6790 
        0.46         1.15        30.28        51.19        24.89        51.78 
TCGA-G7-6796 TCGA-HE-7130 TCGA-MH-A856 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-SX-A7SN 
       71.44        58.19        31.13         6.61        99.12        19.00 
TCGA-SX-A7SQ TCGA-UZ-A9PX TCGA-V9-A7HT TCGA-Y8-A897 
       41.62        65.13        31.73        18.05 

$`13Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U 
       37.15        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        48.85       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-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       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        37.58        38.40        82.45        72.89        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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        7.82         5.98         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       42.41       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5641 TCGA-B2-A4SR 
       31.96        21.30        31.30        31.66        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
        5.46         0.36         0.23        23.31        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        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-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 
       23.47        13.41        24.62        33.47         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-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       129.40        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
       18.15        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       58.75         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       90.54        91.69        55.33        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       16.37        11.70         7.04        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       78.64        15.48        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        25.64        23.28        23.31         0.76        19.63 
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-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       67.73        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 
       33.83        29.03        30.58        34.49        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
       26.40        20.61        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A4JJ 
       79.86        80.88        74.60        34.19        19.00        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       13.08         2.40         1.18         0.43         4.01        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       11.05        39.25        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 
       30.38        27.65        20.25        17.62        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09        42.94        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SP TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       27.06        11.93        16.31        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9Q0 
       98.96        86.27        71.24        30.67        47.47       110.73 
TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY 
       51.35        26.01        39.06        18.64        18.64        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.43               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            133.71             194.79 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             39.80              35.54 
[1] "0.4 - 133.7 (39.8)" "0.1 - 194.8 (35.5)"
[1] "hr=" "1.8"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q GAIN MUTATED        24        6        13        6
  13Q GAIN WILD-TYPE     430       97       177       98
D25V3, multiclass
           clus
vv          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                 24                430
  STAGE II                 6                 97
  STAGE III               13                177
  STAGE IV                 6                 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
  13Q GAIN MUTATED    28   7  17   0
  13Q GAIN WILD-TYPE 452 120 241  15
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1               28                452
  T2                7                120
  T3               17                241
  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    10   3   0
  13Q GAIN WILD-TYPE 313  41   6
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               10                313
  N1                3                 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    27   5
  13Q GAIN WILD-TYPE 519  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     27    5
  13Q GAIN WILD-TYPE  519   84
   clus
vv  13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  0               27                519
  1                5                 84
[1] 2 2
[1] FALSE
D25V7, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    12  40
  13Q GAIN WILD-TYPE 280 550
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     12   40
  13Q GAIN WILD-TYPE  280  550
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               12                280
  MALE                 40                550
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED    28   2
  13Q GAIN WILD-TYPE 380   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     28    2
  13Q GAIN WILD-TYPE  380    1
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                28                380
  YES                2                  1
[1] 2 2
[1] FALSE
D25V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  13Q GAIN MUTATED                    2                                22
  13Q GAIN WILD-TYPE                 64                               506
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  13Q GAIN MUTATED                                      28
  13Q GAIN WILD-TYPE                                   260
D25V10, multiclass
                                       clus
vv                                      13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   22                506
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               28                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"
D25V11, continuous
D25V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q GAIN MUTATED                                  0     1
  13Q GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED                           6    44
  13Q GAIN WILD-TYPE                       115   675
D25V13, multiclass
                                  clus
vv                                 13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       6                115
  WHITE                                          44                675
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V14, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     5  38
  13Q GAIN WILD-TYPE  37 584
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      5   38
  13Q GAIN WILD-TYPE   37  584
                        clus
vv                       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    5                 37
  NOT HISPANIC OR LATINO               38                584
[1] 2 2
[1] FALSE

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                  0   1
  14Q GAIN MUTATED    26  12
  14Q GAIN WILD-TYPE 622 216
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                38                838 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                12                216 
$`14Q GAIN MUTATED`
TCGA-A3-3325 TCGA-BP-4342 TCGA-BP-4799 TCGA-CZ-4865 TCGA-KL-8324 TCGA-KL-8327 
       38.47        74.17        37.25         5.46       153.73       137.06 
TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 
       98.96        24.79        62.37       151.96        49.97        23.47 
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-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3374 
      104.55       103.10        99.88       105.60        96.62        43.20 
TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4699 TCGA-BP-4351 
      112.08        94.19         3.32        28.47         3.62        31.89 
TCGA-BP-4770 TCGA-BP-4994 TCGA-CJ-4901 TCGA-CJ-6028 TCGA-CZ-5460 TCGA-BQ-5880 
       10.82        43.00        47.67        53.42        94.45        43.20 
TCGA-GL-7966 TCGA-HE-7130 
        3.68        58.19 

$`14Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-DV-5565 
       75.58       103.43        46.16         0.59       107.54        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
        6.74        38.07        23.84       109.22        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-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 
       44.91       123.12        51.06        31.33       129.37        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       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
      103.40        92.71        16.67        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       11.90        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61       109.51        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       12.13        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        19.00         1.38        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        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       13.15        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       36.95         3.88        46.45        16.47        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       56.35        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       67.00        62.66       119.64         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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       18.44        79.63        90.54        91.69        55.33        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        22.92        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              3.32               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            153.73             194.79 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             48.82              34.44 
[1] "3.3 - 153.7 (48.8)" "0.1 - 194.8 (34.4)"
[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     442       91       182       97
D26V3, multiclass
           clus
vv          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                 12                442
  STAGE II                12                 91
  STAGE III                8                182
  STAGE IV                 7                 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
  14Q GAIN MUTATED    12  12  12   3
  14Q GAIN WILD-TYPE 468 115 246  12
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1               12                468
  T2               12                115
  T3               12                246
  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 299  42   5
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0               24                299
  N1                2                 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"
D26V6, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    24   5
  14Q GAIN WILD-TYPE 522  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     24    5
  14Q GAIN WILD-TYPE  522   84
   clus
vv  14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  0               24                522
  1                5                 84
[1] 2 2
[1] FALSE
D26V7, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    15  24
  14Q GAIN WILD-TYPE 277 566
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     15   24
  14Q GAIN WILD-TYPE  277  566
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               15                277
  MALE                 24                566
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED    24   0
  14Q GAIN WILD-TYPE 384   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     24    0
  14Q GAIN WILD-TYPE  384    3
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                24                384
  YES                0                  3
[1] 2 2
[1] FALSE
D26V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  14Q GAIN MUTATED                   20                                16
  14Q GAIN WILD-TYPE                 46                               512
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  14Q GAIN MUTATED                                       3
  14Q GAIN WILD-TYPE                                   285
D26V10, multiclass
                                       clus
vv                                      14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  20                 46
  KIDNEY CLEAR CELL RENAL CARCINOMA                   16                512
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                3                285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
D26V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q GAIN MUTATED                                  0     1
  14Q GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED                           2    35
  14Q GAIN WILD-TYPE                       119   684
D26V13, multiclass
                                  clus
vv                                 14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       2                119
  WHITE                                          35                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"
D26V14, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     2  23
  14Q GAIN WILD-TYPE  40 599
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      2   23
  14Q GAIN WILD-TYPE   40  599
                        clus
vv                       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    2                 40
  NOT HISPANIC OR LATINO               23                599
[1] 2 2
[1] FALSE

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                  0   1
  15Q GAIN MUTATED    38  13
  15Q GAIN WILD-TYPE 610 215
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                51                825 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                13                215 
$`15Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-BP-4342 TCGA-AL-A5DJ TCGA-BQ-5892 TCGA-KL-8324 
       28.11        38.47        74.17        49.25        11.97       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        98.96        30.25        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 
       23.47       104.52         3.55        52.27        11.21        42.35 
TCGA-KO-8405 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
      100.47        16.67       104.55        99.88       105.60        96.62 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3430 TCGA-AK-3433 TCGA-B0-4688 
       24.16        43.20        20.28        15.78       112.08         3.32 
TCGA-B0-5081 TCGA-B4-5838 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4337 TCGA-BP-4803 
       11.90         5.46        61.78        54.90         0.07         6.71 
TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5185 TCGA-CJ-4871 TCGA-CJ-4875 
       58.98        43.00         2.04        37.22        79.66       116.84 
TCGA-CJ-4897 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 
      109.84        85.78        66.31       107.41        79.63        94.45 
TCGA-B1-7332 TCGA-P4-A5EB TCGA-Q2-A5QZ 
       37.51        99.12        14.07 

$`15Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       34.29        31.07        42.97        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       28.73        22.45        19.73        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 
       94.72        32.61         3.58        80.68        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 
       21.86        11.87        19.23        26.04        13.25        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07        23.84       109.22        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.33        96.95        92.55        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 
       24.79        73.91        71.41        28.80        54.74        44.91 
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-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.91        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-8406 
       59.08       115.00       100.87       105.47        10.68       103.40 
TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       92.71       103.10        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       74.76        53.29        55.76        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
      109.41        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 
        0.43        89.36        23.05        77.03        62.24        64.27 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       15.62        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 
       36.53        36.39        10.98        36.95        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       36.95         3.88        46.45        16.47        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-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-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       38.30        42.44        37.25        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-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       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 
       78.18        74.66         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
       25.45        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39        93.04        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 
       18.44        90.54        91.69        55.33        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.07               0.10 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
            153.73             194.79 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             52.27              34.29 
[1] "0.1 - 153.7 (52.3)" "0.1 - 194.8 (34.3)"
[1] "hr=" "1.4"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  15Q GAIN MUTATED        17       15        11        9
  15Q GAIN WILD-TYPE     437       88       179       95
D27V3, multiclass
           clus
vv          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                 17                437
  STAGE II                15                 88
  STAGE III               11                179
  STAGE IV                 9                 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
  15Q GAIN MUTATED    17  15  19   1
  15Q GAIN WILD-TYPE 463 112 239  14
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1               17                463
  T2               15                112
  T3               19                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
  15Q GAIN MUTATED    25   4   1
  15Q GAIN WILD-TYPE 298  40   5
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0               25                298
  N1                4                 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"
D27V6, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    32   7
  15Q GAIN WILD-TYPE 514  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     32    7
  15Q GAIN WILD-TYPE  514   82
   clus
vv  15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  0               32                514
  1                7                 82
[1] 2 2
[1] FALSE
D27V7, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    19  33
  15Q GAIN WILD-TYPE 273 557
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     19   33
  15Q GAIN WILD-TYPE  273  557
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               19                273
  MALE                 33                557
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED    30   0
  15Q GAIN WILD-TYPE 378   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     30    0
  15Q GAIN WILD-TYPE  378    3
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                30                378
  YES                0                  3
[1] 2 2
[1] FALSE
D27V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  15Q GAIN MUTATED                   21                                26
  15Q GAIN WILD-TYPE                 45                               502
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  15Q GAIN MUTATED                                       5
  15Q GAIN WILD-TYPE                                   283
D27V10, multiclass
                                       clus
vv                                      15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                   26                502
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                5                283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
D27V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  15Q GAIN MUTATED                                  0     0
  15Q GAIN WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED                           4    48
  15Q GAIN WILD-TYPE                       117   671
D27V13, multiclass
                                  clus
vv                                 15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       4                117
  WHITE                                          48                671
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V14, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     4  31
  15Q GAIN WILD-TYPE  38 591
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      4   31
  15Q GAIN WILD-TYPE   38  591
                        clus
vv                       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               31                591
[1] 2 2
[1] FALSE

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  16P GAIN MUTATED   221  56
  16P GAIN WILD-TYPE 427 172
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
               277                599 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                56                172 
$`16P GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3358 TCGA-B0-4707 TCGA-B0-4712 TCGA-B8-4621 TCGA-BP-4782 
       38.47        42.97        19.73        43.96        25.91        11.64 
TCGA-BP-4995 TCGA-BP-5178 TCGA-CJ-4636 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4W0 
       45.07        62.86        63.25        12.16        37.15        81.21 
TCGA-2Z-A9JJ TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 
       39.88        25.58        16.18        22.49        61.05        21.37 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       12.99        76.64        21.67        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-7046 TCGA-BQ-7058 TCGA-DW-7834 
       11.87        19.23        26.04        96.92        11.28       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 
       35.93        24.46        61.02        17.95        84.89        16.34 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8324 
       17.75        62.83        21.60        15.91        15.62       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        98.96        24.79        62.37       151.96        49.97 
TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 
       23.47        25.48        25.91       104.52         3.55        11.21 
TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       42.35       100.47       104.55       103.10        99.88       105.60 
TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-3387 
       96.62        24.16        37.15        24.16        18.87        20.28 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4811 TCGA-B0-4833 
      112.08        94.19        83.21         3.62        46.59        78.44 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5102 
       27.42        53.88         6.71        43.30        11.90        90.87 
TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 
       52.54        38.63        56.98        42.41       129.67        85.78 
TCGA-B0-5697 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       86.47         1.68        32.98         5.10         1.25         0.53 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-A54E TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 
        5.46        25.55        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-4787 TCGA-BP-4798 
       11.31        12.30        13.15        68.38        15.78        10.98 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 
        6.71        47.97        71.41         6.74        58.98        48.89 
TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5173 
       49.38        14.93        36.07         3.88        43.00         2.04 
TCGA-BP-5175 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4873 
       30.64        19.82        34.95        11.05        79.66        74.27 
TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 
      116.84       113.46        63.98       109.84        47.67        51.29 
TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 
       49.28       131.08        72.00       133.71        22.32       122.83 
TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4858 
       62.10        53.42        92.02        66.31        74.66        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 
       58.75         6.77       107.41        23.74        79.63        90.54 
TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX TCGA-EU-5905 
       94.45         2.40        31.10        67.96        53.46         3.91 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JP 
        7.04        75.55        58.22       100.27        56.91        29.36 
TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 
        5.29        12.82       106.55        49.58        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7583 
       71.80        62.93        19.36        27.09        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
       35.18        16.64        30.48        25.64        23.97        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-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU 
        8.48        16.31        15.75         9.63        49.32         2.20 
TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       41.13        30.58        12.46        28.18         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 
       43.99        22.06         0.16        12.30        86.76        43.20 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 
       47.80        25.35         7.66         0.95       123.62        48.26 
TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-EV-5902 
       50.40         7.04         3.81        40.77        51.19        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-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 
       51.78        25.15        17.98        23.08       194.79         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-A5NI 
       27.65         1.05        12.89        11.21        81.93        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83V 
       56.75        25.22        16.80         2.04        85.78        96.69 
TCGA-IZ-8195 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       22.26        12.36        18.41        29.10        11.41        34.29 
TCGA-MH-A560 TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       30.38        17.62        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71U 
       99.12        52.27        50.60        78.90        47.90        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       28.80        27.06        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
       53.10       117.40       125.29        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A897 
       47.47        65.13       110.73        51.35        31.73        18.05 
TCGA-Y8-A8S0 
        6.02 

$`16P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       47.21        34.29        31.07        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       28.73        22.45        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 
       15.78        70.68       119.38       126.05        24.82         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
        8.42        15.42       111.02        94.72        32.61         3.58 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 
       80.68        74.17        54.77        12.33        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       60.59        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       25.81        27.22         5.82        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       48.10        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL 
       23.90        70.13        23.01        75.42        34.85        33.07 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7734 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-BQ-5888 
       12.26        67.17         0.89        49.25        27.68        13.25 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 
       11.97        44.84        26.27        20.12        48.85        13.61 
TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-IA-A83W 
       37.55        13.78         3.75        14.63         3.02        67.17 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A8RZ 
       12.13        29.26        19.73        41.33        86.37         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07        23.84       109.22        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 
       66.54        73.91        71.41        28.80        54.74        44.91 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 
      123.12        51.06        31.33       129.37        87.91        65.19 
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-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 
      115.00       100.87       105.47        10.68       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       16.67        90.48        92.55        12.66        11.90        36.82 
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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI 
       55.76        20.71        18.64        28.31        65.52        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
       68.61       109.51        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        37.58        38.40        82.45        72.89        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-B0-4700 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        57.70         6.64         3.25        58.45 
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-B0-4828 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4842 TCGA-B0-4843 
       10.09        68.71        40.70        45.30        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 
       36.85        70.52        20.94        11.24         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       15.95        62.89        90.48        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       48.82        46.39       111.52       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46        32.61        35.90        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        31.66        21.57        16.67        12.00         5.75 
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        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 
       42.71        25.05        45.37        17.19        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       17.06         1.74        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 
       90.28        99.85        23.05        77.03        62.24        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       21.21        15.62        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 
       44.94        12.23        33.99        31.33        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        5.33        61.97        13.51        56.91        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       36.53        36.39        36.95        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4974 
       60.30        61.22        57.40        14.24        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 
       47.11        33.34        46.45        31.30        36.95        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 
       35.21        28.87         6.35        79.30        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       33.47         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16       114.41        54.61        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-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       115.69 
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-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-5680 
        4.57        18.81       129.40        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       18.15        73.35        67.00        62.66       119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       18.44        91.69        55.33        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       69.96        84.30        22.52         1.94        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ 
       65.65        12.26        14.63        22.78        62.63        12.00 
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-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J2 
        2.01        19.43        19.96        16.37        11.70        59.01 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JZ 
       30.71        24.33        31.20         0.13        11.57        90.21 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 
       15.48        43.04        12.99        12.39        67.43        19.63 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A5Y0 
       19.13         7.82         0.23        29.46        23.28         8.28 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 
       12.46        70.19        66.71        62.66        67.73        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E 
       34.49        50.50        26.40        20.61        17.23        14.86 
TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 
       17.49        19.27         8.88        63.72        22.92        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       40.83        26.04        30.28        10.82         7.92         2.76 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 
       93.34        61.28        49.84         7.63         7.17        79.86 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 TCGA-G7-6793 
       80.88        74.60        34.19        10.68        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
       39.25        71.44        20.52        25.84        25.25        16.90 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NH 
       80.65        12.92        12.43        16.31        58.19        26.01 
TCGA-HE-A5NK TCGA-IA-A40X TCGA-IA-A83T TCGA-IZ-8196 TCGA-J7-6720 TCGA-J7-8537 
       73.25        19.99        88.24        21.34        12.76        10.55 
TCGA-J7-A8I2 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 TCGA-O9-A75Z 
       10.09        27.78        27.65        20.25        31.13        15.48 
TCGA-P4-A5ED TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM TCGA-SX-A7SU 
       92.58        16.01        14.07        49.45        11.93        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-A9G9 
       18.02        26.20       103.63        37.35        86.27        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       39.06        18.64        18.64        25.28        13.28 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.07               0.10 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            194.79             149.16 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             30.67              36.85 
[1] "0.1 - 194.8 (30.7)" "0.1 - 149.2 (36.9)"
[1] "hr=" "1.4"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P GAIN MUTATED       145       30        60       29
  16P GAIN WILD-TYPE     309       73       130       75
D28V3, multiclass
           clus
vv          16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                145                309
  STAGE II                30                 73
  STAGE III               60                130
  STAGE IV                29                 75
[1] 4 2
[1] TRUE
[1] "dimension of 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   158  38  79   5
  16P GAIN WILD-TYPE 322  89 179  10
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1              158                322
  T2               38                 89
  T3               79                179
  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    90  14   3
  16P GAIN WILD-TYPE 233  30   3
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               90                233
  N1               14                 30
  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   143  22
  16P GAIN WILD-TYPE 403  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    143   22
  16P GAIN WILD-TYPE  403   67
   clus
vv  16P GAIN MUTATED 16P GAIN WILD-TYPE
  0              143                403
  1               22                 67
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    73 208
  16P GAIN WILD-TYPE 219 382
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     73  208
  16P GAIN WILD-TYPE  219  382
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               73                219
  MALE                208                382
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED   156   2
  16P GAIN WILD-TYPE 252   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED    156    2
  16P GAIN WILD-TYPE  252    1
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO               156                252
  YES                2                  1
[1] 2 2
[1] FALSE
D28V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16P GAIN MUTATED                   21                               107
  16P GAIN WILD-TYPE                 45                               421
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16P GAIN MUTATED                                     153
  16P GAIN WILD-TYPE                                   135
D28V10, multiclass
                                       clus
vv                                      16P GAIN MUTATED 16P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  107                421
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              153                135
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
D28V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16P GAIN MUTATED                                  2     5
  16P GAIN WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED                          29   238
  16P GAIN WILD-TYPE                        92   481
D28V13, multiclass
                                  clus
vv                                 16P GAIN MUTATED 16P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           5                 11
  BLACK OR AFRICAN AMERICAN                      29                 92
  WHITE                                         238                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"
D28V14, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    12 206
  16P GAIN WILD-TYPE  30 416
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     12  206
  16P GAIN WILD-TYPE   30  416
                        clus
vv                       16P GAIN MUTATED 16P GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 30
  NOT HISPANIC OR LATINO              206                416
[1] 2 2
[1] FALSE

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED   215  49
  16Q GAIN WILD-TYPE 433 179
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
               264                612 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                49                179 
$`16Q GAIN MUTATED`
TCGA-A3-3325 TCGA-A3-3358 TCGA-B0-4707 TCGA-B0-4712 TCGA-B8-4621 TCGA-BP-4782 
       38.47        42.97        19.73        43.96        25.91        11.64 
TCGA-BP-5178 TCGA-CJ-4636 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-A4W0 TCGA-2Z-A9JJ 
       62.86        63.25        12.16        37.15        81.21        39.88 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 TCGA-AL-3468 
       25.58        16.18        22.49        61.05        21.37        76.64 
TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       21.67        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-7046 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DZ-6134 
       26.04        96.92       129.86        35.93        24.46        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ 
       17.95        84.89        16.34        17.75        62.83        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 
       15.91        15.62       153.73       137.06        98.96        24.79 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8422 TCGA-KN-8423 
       62.37       151.96        49.97        23.47        25.48        25.91 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8409 
      104.52         3.55        11.21        42.35       100.47       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 TCGA-A3-3382 
      103.10        99.88       105.60        96.62        24.16        18.87 
TCGA-A3-3387 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-4811 
       20.28       112.08        94.19        83.21         3.62        46.59 
TCGA-B0-4833 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5102 
       78.44        27.42        53.88        43.30        11.90        90.87 
TCGA-B0-5106 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       52.54        38.63        56.98       129.67        85.78        86.47 
TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-A54E 
        1.68         5.10         1.25         5.46        25.55        29.88 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4174 
        4.93       101.06        93.34         0.43        89.36        61.78 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4768 
        0.07        93.99        31.89        11.31        12.30        13.15 
TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       68.38        15.78        10.98         6.71        47.97        71.41 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4977 TCGA-BP-4981 
        6.74        58.98        48.89        49.38        14.93        36.07 
TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5198 TCGA-BP-5200 
        3.88        43.00         2.04        30.64        19.82        34.95 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4885 TCGA-CJ-4889 
       11.05        79.66        74.27       116.84       113.46        63.98 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5672 
      109.84        47.67        51.29        49.28       131.08        72.00 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6028 TCGA-CW-5581 
      133.71        22.32       122.83        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       107.41 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5984 
       79.63        90.54        94.45         2.40        31.10        67.96 
TCGA-DV-A4VX TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       53.46         3.91         7.04        75.55        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9JY 
       56.91        29.36         5.29        12.82       106.55        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9KE TCGA-A4-7286 
       22.26        78.64        71.80        62.93        27.09        18.21 
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-3471 TCGA-AT-A5NU 
       16.96         8.48        16.31        15.75        49.32         2.20 
TCGA-B1-5398 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 
       41.13        30.58        12.46        28.18         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5880 
       43.99        22.06         0.16        12.30        86.76        43.20 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7051 
       47.80        25.35         0.95       123.62        48.26        50.40 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-EV-5902 TCGA-EV-5903 
        7.04         3.81        40.77        51.19        19.00        24.89 
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-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       25.15        17.98        23.08       194.79         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 TCGA-HE-A5NI TCGA-HE-A5NL 
        1.05        12.89        11.21        81.93        11.84        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99         2.04        85.78        96.69        22.26 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A560 
       12.36        18.41        29.10        11.41        34.29        30.38 
TCGA-MH-A854 TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       17.62        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V 
       52.27        50.60        78.90        47.90        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        53.10 
TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      117.40       125.29        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-Y8-A897 TCGA-Y8-A8S0 
       65.13       110.73        51.35        31.73        18.05         6.02 

$`16Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       47.21        34.29        31.07        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       28.73        22.45        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 
       15.78        70.68       119.38       126.05        24.82         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
        8.42        15.42       111.02        94.72        32.61         3.58 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 
       80.68        74.17        54.77        12.33        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       60.59        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       35.90        48.10        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       31.27       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 
        5.46        43.69        45.96        65.88        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       56.84        23.90        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       33.07        12.26        67.17         0.89        12.99        49.25 
TCGA-B1-A47O TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       27.68        13.25        11.97        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       11.28        48.85        13.61        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       14.63         3.02        67.17        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       41.33        86.37         6.74        38.07        23.84       109.22 
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-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       28.80        54.74        44.91       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
      129.37        87.91        65.19         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       105.47 
TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8416 TCGA-KO-8417 
       10.68       103.40        92.71        16.67        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-A6NI TCGA-A3-A6NJ 
       20.71        18.64        28.31        65.52        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
      109.51        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         1.38        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        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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-B0-4834 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       68.71        40.70        45.30         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 
       36.85        70.52        20.94        11.24         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       15.95        62.89        90.48        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5699 TCGA-B0-5701 
       48.82        46.39        42.41       111.52       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 
      131.15        89.49        91.46        32.61        35.90        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
       12.00         5.75         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        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       17.19        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J 
       34.39        14.30        27.29        17.06         1.74        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 
       16.27        14.17        85.51        90.28        99.85        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       77.03        62.24        64.27        54.90        97.45        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 
       27.78        62.07        37.25        21.21        15.62        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 
       52.24        62.86        49.08        44.94        12.23        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       31.33        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4801 
       56.91        60.95        48.95        36.53        36.39        36.95 
TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 
       87.45        63.62        58.68        60.30        61.22        57.40 
TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4982 TCGA-BP-4983 
       14.24        45.50         6.94        47.11        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       31.30        36.95        46.45        16.47        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       79.30        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-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 
       23.47        13.41        24.62        33.47         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 
       58.95        21.24        83.97        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-4887 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       30.64        51.52       115.69        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       50.24        56.35        49.97        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       129.40 
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-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 
       62.66       119.64         7.36        64.57        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 
       85.78        73.18        78.18         1.35       105.93        83.90 
TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       18.77        25.45        47.08        14.66        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 
       63.42        58.82        79.53        23.74        18.44        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       55.33        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       22.52         1.94        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       14.63        22.78        62.63        12.00        18.12         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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J2 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       19.96        16.37        11.70        59.01         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 
       31.20         0.13        11.57        90.21        15.48        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7732 
       19.36        12.99        12.39        67.43        19.63        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A5Y0 TCGA-A4-A6HP 
        7.82         0.23        29.46        23.28         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-7332 
        9.63        70.19        66.71        62.66        67.73        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E 
       34.49        50.50        26.40        20.61        17.23        14.86 
TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5882 
       17.49        19.27         8.88        63.72        22.92        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 
       40.83        26.04        30.28        10.82         7.66         7.92 
TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 
        2.76        93.34        61.28        49.84         7.63         7.17 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A4JJ TCGA-G7-6792 
       79.86        80.88        74.60        34.19        10.68        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       11.05        39.25        71.44        20.52        25.84        25.25 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-A59R TCGA-GL-A9DE TCGA-HE-7130 
       16.90        80.65        12.92        12.43        16.31        58.19 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A83T TCGA-IZ-8196 TCGA-J7-6720 
       26.01        56.75        73.25        88.24        21.34        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 
       10.55        10.09        27.78        27.65        20.25        31.13 
TCGA-O9-A75Z TCGA-P4-A5ED TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A7SM 
       15.48        92.58        16.01        14.07        49.45        11.93 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PN TCGA-UZ-A9PQ 
       43.76        18.02        26.20       103.63        37.35        86.27 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       26.01        39.06        18.64        18.64        25.28        13.28 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.07               0.10 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            194.79             149.16 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            31.415             36.530 
[1] "0.1 - 194.8 (31.4)" "0.1 - 149.2 (36.5)"
[1] "hr=" "1.6"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q GAIN MUTATED       143       30        56       24
  16Q GAIN WILD-TYPE     311       73       134       80
D29V3, multiclass
           clus
vv          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                143                311
  STAGE II                30                 73
  STAGE III               56                134
  STAGE IV                24                 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
  16Q GAIN MUTATED   154  36  73   4
  16Q GAIN WILD-TYPE 326  91 185  11
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1              154                326
  T2               36                 91
  T3               73                185
  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    86  12   2
  16Q GAIN WILD-TYPE 237  32   4
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               86                237
  N1               12                 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"
D29V6, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   135  18
  16Q GAIN WILD-TYPE 411  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    135   18
  16Q GAIN WILD-TYPE  411   71
   clus
vv  16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  0              135                411
  1               18                 71
[1] 2 2
[1] FALSE
D29V7, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    72 196
  16Q GAIN WILD-TYPE 220 394
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     72  196
  16Q GAIN WILD-TYPE  220  394
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               72                220
  MALE                196                394
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED   152   1
  16Q GAIN WILD-TYPE 256   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED    152    1
  16Q GAIN WILD-TYPE  256    2
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO               152                256
  YES                1                  2
[1] 2 2
[1] FALSE
D29V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16Q GAIN MUTATED                   21                                99
  16Q GAIN WILD-TYPE                 45                               429
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16Q GAIN MUTATED                                     148
  16Q GAIN WILD-TYPE                                   140
D29V10, multiclass
                                       clus
vv                                      16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                   99                429
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              148                140
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
D29V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q GAIN MUTATED                                  2     5
  16Q GAIN WILD-TYPE                                0    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED                          30   225
  16Q GAIN WILD-TYPE                        91   494
D29V13, multiclass
                                  clus
vv                                 16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           5                 11
  BLACK OR AFRICAN AMERICAN                      30                 91
  WHITE                                         225                494
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V14, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    12 196
  16Q GAIN WILD-TYPE  30 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     12  196
  16Q GAIN WILD-TYPE   30  426
                        clus
vv                       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  HISPANIC OR LATINO                   12                 30
  NOT HISPANIC OR LATINO              196                426
[1] 2 2
[1] FALSE

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                  0   1
  17P GAIN MUTATED   166  27
  17P GAIN WILD-TYPE 482 201
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
               193                683 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                27                201 
$`17P GAIN MUTATED`
TCGA-A3-3325 TCGA-B8-4621 TCGA-2Z-A9JD TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       38.47        25.91        34.85        25.58        16.18        22.49 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5892 TCGA-BQ-7046 
       21.07        10.16        21.86        19.23        11.97        96.92 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       84.89        16.34        17.75        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3453 TCGA-B0-4696 
       15.91        15.62        24.16        10.49        83.21        28.47 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5838 TCGA-B8-5551 TCGA-BP-4177 TCGA-BP-4756 
       90.87        19.30         5.46         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         2.04        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       107.41        31.10         3.91 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       56.91         4.57        56.81        30.71        29.36         5.29 
TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
        0.13        49.58        90.21        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8310 
       62.93        27.09        18.21        19.13        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-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3471 
       16.96        16.31        15.75         8.28        12.46        49.32 
TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 
       66.71         2.20        37.51        36.49        20.25        33.83 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       30.58        12.46        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5881 
        1.15        43.99        22.06         0.16        17.49        47.80 
TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7051 TCGA-BQ-7060 
       25.35         0.95         7.92        48.26        50.40         7.04 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 
        3.81        40.77        51.19        34.19        24.89        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
        2.40         1.18        51.78        39.25        71.44        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
        3.68         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       26.01        11.84        56.75        25.22        16.80         2.04 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA 
       30.38        27.65        20.25        15.48        87.09         6.61 
TCGA-P4-A5EB TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       99.12        47.90        49.45        44.61        28.80        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      117.40       103.63       125.29        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A8RY 
       47.47        65.13       110.73        31.73        39.06        25.28 
TCGA-Y8-A8S0 
        6.02 

$`17P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
      126.05        24.82         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       62.86        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV 
       23.01        75.42        39.88        33.07        12.26        67.17 
TCGA-A4-A5Y1 TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 
       12.99        27.68        11.87        26.04        13.25        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 
       26.27        20.12        11.28        67.17        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       19.73        41.33         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         0.53 
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       39.16        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-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        51.25 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 
       46.78        48.36        78.64        40.01        94.29        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
        5.75         5.10         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        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       48.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 
       23.05        77.03        62.24        61.78        64.27        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        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-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-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-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 
       13.41        24.62        33.47        19.82         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       47.18        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 
       50.24        56.35        49.97        51.29        49.18        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 
       78.18        74.66         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
       25.45        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39        93.04        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG 
        2.01        19.43        19.96        16.37        91.73        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y 
       51.52        38.99        24.33        31.20        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
      106.55        15.48        43.04        19.36        12.99        12.39 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       67.43        19.63         0.10        35.18         7.82         0.23 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3466 
       30.48        29.46        23.28        12.46         8.48         9.63 
TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 
       70.19        62.66        67.73        41.13        16.77        20.32 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI 
       29.03        34.49        20.61        17.23        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-5889 TCGA-BQ-5890 
       21.63        40.83        26.04        30.28        10.82         7.66 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 
        2.76       123.62        93.34        61.28        49.84         7.63 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
        7.17        79.86        80.88        74.60        19.00        10.68 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 
        0.43         4.01        90.90        11.05        25.15        20.52 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40X 
       12.92        27.65        16.31        58.19        73.25        19.99 
TCGA-IA-A83S TCGA-J7-A8I2 TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 
       85.78        10.09        17.62        31.13        99.78        42.94 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9Q1 
       27.06        11.93        18.02        37.35        86.27        51.35 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S1 
       26.01        18.64        18.64        18.05        13.28 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.13               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            194.79             153.73 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             25.64              38.70 
[1] "0.1 - 194.8 (25.6)" "0.1 - 153.7 (38.7)"
[1] "hr=" "1.7"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P GAIN MUTATED       131       19        23        6
  17P GAIN WILD-TYPE     323       84       167       98
D30V3, multiclass
           clus
vv          17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                131                323
  STAGE II                19                 84
  STAGE III               23                167
  STAGE IV                 6                 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
  17P GAIN MUTATED   141  26  26   2
  17P GAIN WILD-TYPE 339 101 232  13
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1              141                339
  T2               26                101
  T3               26                232
  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   0
  17P GAIN WILD-TYPE 291  33   6
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0               32                291
  N1               11                 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"
D30V6, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    68   3
  17P GAIN WILD-TYPE 478  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     68    3
  17P GAIN WILD-TYPE  478   86
   clus
vv  17P GAIN MUTATED 17P GAIN WILD-TYPE
  0               68                478
  1                3                 86
[1] 2 2
[1] FALSE
D30V7, binary
                    cls
clus                   0   1
  17P GAIN MUTATED    44 152
  17P GAIN WILD-TYPE 248 438
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     44  152
  17P GAIN WILD-TYPE  248  438
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               44                248
  MALE                152                438
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED   132   1
  17P GAIN WILD-TYPE 276   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED    132    1
  17P GAIN WILD-TYPE  276    2
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO               132                276
  YES                1                  2
[1] 2 2
[1] FALSE
D30V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17P GAIN MUTATED                    0                                25
  17P GAIN WILD-TYPE                 66                               503
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17P GAIN MUTATED                                     171
  17P GAIN WILD-TYPE                                   117
D30V10, multiclass
                                       clus
vv                                      17P GAIN MUTATED 17P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   25                503
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              171                117
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
D30V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P GAIN MUTATED                                  2     6
  17P GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED                          33   147
  17P GAIN WILD-TYPE                        88   572
D30V13, multiclass
                                  clus
vv                                 17P GAIN MUTATED 17P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           6                 10
  BLACK OR AFRICAN AMERICAN                      33                 88
  WHITE                                         147                572
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V14, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     4 168
  17P GAIN WILD-TYPE  38 454
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4  168
  17P GAIN WILD-TYPE   38  454
                        clus
vv                       17P GAIN MUTATED 17P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO              168                454
[1] 2 2
[1] FALSE

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED   182  37
  17Q GAIN WILD-TYPE 466 191
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
               219                657 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                37                191 
$`17Q GAIN MUTATED`
TCGA-A3-3325 TCGA-B0-4707 TCGA-B8-4621 TCGA-G6-A8L7 TCGA-2Z-A9JD TCGA-2Z-A9JQ 
       38.47        19.73        25.91        70.13        34.85        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       16.18        22.49        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IZ-A6M8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR 
       17.95        84.89        16.34        17.75        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3453 
       21.60        15.91        15.62        24.16        10.49        83.21 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5551 
       90.87        19.30         0.53         5.46        23.31         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         2.04        38.30        37.22        34.95        74.27 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5469 TCGA-EU-5905 
       47.67        49.28         6.77       107.41        31.10         3.91 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-2Z-A9JP 
       56.91         4.57        56.81        51.52        30.71        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
        5.29         0.13        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KE TCGA-A4-7286 
       15.48        71.80        62.93        19.36        27.09        18.21 
TCGA-A4-7732 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
       19.13         0.23        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-3466 TCGA-AL-3471 TCGA-AL-3472 
       15.75         8.28        12.46         9.63        49.32        66.71 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 
        2.20        37.51        36.49        20.25        16.77        33.83 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       30.58        12.46        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 
        1.15        43.99        22.06         0.16        17.49        86.76 
TCGA-BQ-5881 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 
       47.80        25.35         7.66         0.95         7.92        48.26 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 
       50.40        49.84         7.04         3.81        40.77        80.88 
TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       51.19        34.19        24.89        13.08         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 
        4.01        51.78        11.05        39.25        71.44        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-7129 
        3.68         1.05        12.43        12.89        11.21        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y 
       26.01        11.84        56.75        25.22        16.80         2.04 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.55        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EA 
       30.38        27.65        20.25        15.48        87.09         6.61 
TCGA-P4-A5EB TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       99.12        16.01        14.07        47.90        49.45        44.61 
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        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP 
       43.76        26.20       117.40       103.63       125.29        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-V9-A7HT 
       71.24        30.67        47.47        65.13       110.73        31.73 
TCGA-WN-AB4C TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        25.28         6.02 

$`17Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       24.82         1.18         8.42        15.42       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       32.61         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-MM-A84U TCGA-2Z-A9J9 
       66.28        56.84        23.90        81.21        23.01        75.42 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-BQ-7049 
       39.88        33.07        12.26        67.17        12.99        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-IA-A83W TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       26.27        20.12        67.17        12.13        29.26        19.73 
TCGA-SX-A7SO TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       41.33         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       92.55        12.66        11.90        36.82         0.53        39.16 
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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 
       45.53        29.92        18.44        88.37        51.25        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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-3430 
       10.62        29.10       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       73.68       112.08        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 
       48.36        78.64        40.01        94.29        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         5.10         1.25         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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        50.14        16.60         6.38        48.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        21.21        15.62        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       11.31        33.99        31.33        77.98         5.98        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-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-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-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       74.40        42.44        37.25        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        19.82         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
      109.84        50.24        56.35        49.97        51.29        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       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39        93.04        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG 
        2.01        19.43        19.96        16.37        91.73        54.64 
TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       38.99        24.33        31.20        12.82        11.57       106.55 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 
       43.04        12.99        12.39        67.43        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-A48D 
       35.18         7.82        30.48        29.46        23.28        12.46 
TCGA-A4-A57E TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 
        8.48        70.19        62.66        67.73        41.13        20.32 
TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI 
       29.03        34.49        20.61        17.23        14.86        12.30 
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-5889 TCGA-BQ-5894 TCGA-BQ-7044 
       40.83        26.04        30.28        10.82         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6135 
       93.34        61.28         7.63         7.17        79.86        74.60 
TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 
       19.00        10.68         0.43        90.90        25.15        20.52 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40X 
       12.92        27.65        16.31        58.19        73.25        19.99 
TCGA-IA-A83S TCGA-J7-A8I2 TCGA-MH-A854 TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5E8 
       85.78        10.09        17.62        31.13        99.78        42.94 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A7SL TCGA-SX-A7SM 
       92.58        52.27        50.60        78.90        27.06        11.93 
TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 
       18.02        37.35        86.27        51.35        26.01        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8S1 
       18.64        18.05        13.28 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.10 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
            194.79             153.73 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             25.22              40.01 
[1] "0.1 - 194.8 (25.2)" "0.1 - 153.7 (40.0)"
[1] "hr=" "1.3"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q GAIN MUTATED       139       20        33       11
  17Q GAIN WILD-TYPE     315       83       157       93
D31V3, multiclass
           clus
vv          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                139                315
  STAGE II                20                 83
  STAGE III               33                157
  STAGE IV                11                 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
  17Q GAIN MUTATED   149  28  41   3
  17Q GAIN WILD-TYPE 331  99 217  12
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1              149                331
  T2               28                 99
  T3               41                217
  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 GAIN MUTATED    42  12   3
  17Q GAIN WILD-TYPE 281  32   3
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               42                281
  N1               12                 32
  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    79   6
  17Q GAIN WILD-TYPE 467  83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     79    6
  17Q GAIN WILD-TYPE  467   83
   clus
vv  17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  0               79                467
  1                6                 83
[1] 2 2
[1] FALSE
D31V7, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    58 164
  17Q GAIN WILD-TYPE 234 426
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     58  164
  17Q GAIN WILD-TYPE  234  426
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               58                234
  MALE                164                426
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED   142   1
  17Q GAIN WILD-TYPE 266   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED    142    1
  17Q GAIN WILD-TYPE  266    2
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO               142                266
  YES                1                  2
[1] 2 2
[1] FALSE
D31V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17Q GAIN MUTATED                    0                                32
  17Q GAIN WILD-TYPE                 66                               496
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17Q GAIN MUTATED                                     190
  17Q GAIN WILD-TYPE                                    98
D31V10, multiclass
                                       clus
vv                                      17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   0                 66
  KIDNEY CLEAR CELL RENAL CARCINOMA                   32                496
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              190                 98
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
D31V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q GAIN MUTATED                                  2     6
  17Q GAIN WILD-TYPE                                0    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED                          38   167
  17Q GAIN WILD-TYPE                        83   552
D31V13, multiclass
                                  clus
vv                                 17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                2                  0
  ASIAN                                           6                 10
  BLACK OR AFRICAN AMERICAN                      38                 83
  WHITE                                         167                552
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V14, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     6 185
  17Q GAIN WILD-TYPE  36 437
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      6  185
  17Q GAIN WILD-TYPE   36  437
                        clus
vv                       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    6                 36
  NOT HISPANIC OR LATINO              185                437
[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 601 221
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                54                822 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                221 
$`18P GAIN MUTATED`
TCGA-A3-3325 TCGA-B0-5693 TCGA-BP-4342 TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-DW-5560 
       38.47       133.94        74.17        12.99        21.86        48.85 
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 
      153.73       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-A3-3374 
      100.47       104.55       103.10        96.62         0.53        43.20 
TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4710 TCGA-B0-5113 TCGA-B2-5633 TCGA-B4-5838 
       18.87       112.08        57.70        38.63        31.66         5.46 
TCGA-BP-4177 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 
       54.90        31.89        13.15        48.95        16.47        46.55 
TCGA-CJ-4872 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 
       47.18       109.84        49.18        64.57        81.83        85.78 
TCGA-CZ-5457 TCGA-CZ-5467 TCGA-2Z-A9J1 TCGA-AL-3466 TCGA-B3-4103 TCGA-B3-4104 
       90.54         2.40        75.55         9.63        30.58        34.49 
TCGA-G7-6790 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-HE-7130 TCGA-HE-A5NJ TCGA-SX-A7SS 
       51.78        17.98        23.08        58.19        56.75        53.10 

$`18P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
       18.51       112.80        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 
       94.72        32.61         3.58        80.68        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       109.22        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
       44.91        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       105.47        10.68       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67        99.88       105.60        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        11.90        36.82        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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4713 TCGA-B0-4714 
       65.10         7.82         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 
       35.90         1.68        31.96        21.30        31.30        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       15.78        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       63.98       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4908 
       56.35        47.67        49.97        51.29        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 
       67.00        53.42        62.66       119.64         7.36        92.02 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       58.75         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        16.37        11.70         7.04        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       18.21        19.63         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
       12.46        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       20.32        33.83        29.03        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43         4.01        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.53               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
            153.73             194.79 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             48.90              34.34 
[1] "0.5 - 153.7 (48.9)" "0.1 - 194.8 (34.3)"
[1] "hr=" "2.6"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P GAIN MUTATED        26       10        11        6
  18P GAIN WILD-TYPE     428       93       179       98
D32V3, multiclass
           clus
vv          18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                 26                428
  STAGE II                10                 93
  STAGE III               11                179
  STAGE IV                 6                 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
  18P GAIN MUTATED    28  11  15   0
  18P GAIN WILD-TYPE 452 116 243  15
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1               28                452
  T2               11                116
  T3               15                243
  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
  18P GAIN MUTATED    26   3   0
  18P GAIN WILD-TYPE 297  41   6
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0               26                297
  N1                3                 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"
D32V6, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    36   4
  18P GAIN WILD-TYPE 510  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     36    4
  18P GAIN WILD-TYPE  510   85
   clus
vv  18P GAIN MUTATED 18P GAIN WILD-TYPE
  0               36                510
  1                4                 85
[1] 2 2
[1] FALSE
D32V7, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    21  33
  18P GAIN WILD-TYPE 271 557
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     21   33
  18P GAIN WILD-TYPE  271  557
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               21                271
  MALE                 33                557
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED    34   0
  18P GAIN WILD-TYPE 374   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     34    0
  18P GAIN WILD-TYPE  374    3
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                34                374
  YES                0                  3
[1] 2 2
[1] FALSE
D32V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18P GAIN MUTATED                   16                                25
  18P GAIN WILD-TYPE                 50                               503
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18P GAIN MUTATED                                      13
  18P GAIN WILD-TYPE                                   275
D32V10, multiclass
                                       clus
vv                                      18P GAIN MUTATED 18P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  16                 50
  KIDNEY CLEAR CELL RENAL CARCINOMA                   25                503
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               13                275
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
D32V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P GAIN MUTATED                                  0     0
  18P GAIN WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED                           2    50
  18P GAIN WILD-TYPE                       119   669
D32V13, multiclass
                                  clus
vv                                 18P GAIN MUTATED 18P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       2                119
  WHITE                                          50                669
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V14, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     4  34
  18P GAIN WILD-TYPE  38 588
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      4   34
  18P GAIN WILD-TYPE   38  588
                        clus
vv                       18P GAIN MUTATED 18P GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               34                588
[1] 2 2
[1] FALSE

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                  0   1
  18Q GAIN MUTATED    44   6
  18Q GAIN WILD-TYPE 604 222
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                50                826 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                222 
$`18Q GAIN MUTATED`
TCGA-A3-3325 TCGA-B0-4707 TCGA-B0-5693 TCGA-BP-4342 TCGA-B9-5155 TCGA-DW-5560 
       38.47        19.73       133.94        74.17        21.86        48.85 
TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8419 
      153.73       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-A3-3374 
      100.47       104.55       103.10        96.62         0.53        43.20 
TCGA-A3-3382 TCGA-AK-3433 TCGA-B0-4710 TCGA-B0-5113 TCGA-B2-5633 TCGA-B4-5838 
       18.87       112.08        57.70        38.63        31.66         5.46 
TCGA-BP-4177 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4789 TCGA-BP-4992 TCGA-CJ-4635 
       54.90        31.89        13.15        48.95        16.47        46.55 
TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5585 TCGA-CZ-5457 
      109.84        49.18        64.57        81.83        85.78        90.54 
TCGA-CZ-5467 TCGA-2Z-A9J1 TCGA-B3-4103 TCGA-B3-4104 TCGA-G7-6790 TCGA-G7-A8LB 
        2.40        75.55        30.58        34.49        51.78        17.98 
TCGA-G7-A8LC TCGA-SX-A7SS 
       23.08        53.10 

$`18Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      112.80        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       25.91         1.18         8.42        15.42       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
       32.61         3.58        80.68        54.77        12.33        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      103.43        46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 
       44.84        26.27        20.12        11.28        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       109.22        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KN-8418 TCGA-KN-8421 
       44.91        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       105.47        10.68       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 
       92.71        16.67        99.88       105.60        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        11.90        36.82        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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4713 TCGA-B0-4714 
       65.10         7.82         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 
       35.90         1.68        31.96        21.30        31.30        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        64.27        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       62.07        37.25        21.21        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       15.78        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 
       50.24        56.35        47.67        49.97        51.29        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       21.76        69.96        84.30        22.52         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J2 
       19.43        19.96        16.37        11.70         7.04        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-8121 
       20.25        16.77        20.32        33.83        29.03        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.84        25.25        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 
       19.00        16.31        41.62        26.47        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.53               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
            153.73             194.79 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             48.90              34.62 
[1] "0.5 - 153.7 (48.9)" "0.1 - 194.8 (34.6)"
[1] "hr=" "2.9"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q GAIN MUTATED        25       10        10        5
  18Q GAIN WILD-TYPE     429       93       180       99
D33V3, multiclass
           clus
vv          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                 25                429
  STAGE II                10                 93
  STAGE III               10                180
  STAGE IV                 5                 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
  18Q GAIN MUTATED    25  11  14   0
  18Q GAIN WILD-TYPE 455 116 244  15
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1               25                455
  T2               11                116
  T3               14                244
  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 298  43   6
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0               25                298
  N1                1                 43
  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 512  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     34    3
  18Q GAIN WILD-TYPE  512   86
   clus
vv  18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  0               34                512
  1                3                 86
[1] 2 2
[1] FALSE
D33V7, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    20  30
  18Q GAIN WILD-TYPE 272 560
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     20   30
  18Q GAIN WILD-TYPE  272  560
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               20                272
  MALE                 30                560
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED    31   0
  18Q GAIN WILD-TYPE 377   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     31    0
  18Q GAIN WILD-TYPE  377    3
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                31                377
  YES                0                  3
[1] 2 2
[1] FALSE
D33V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18Q GAIN MUTATED                   16                                25
  18Q GAIN WILD-TYPE                 50                               503
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18Q GAIN MUTATED                                       9
  18Q GAIN WILD-TYPE                                   279
D33V10, multiclass
                                       clus
vv                                      18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  16                 50
  KIDNEY CLEAR CELL RENAL CARCINOMA                   25                503
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                9                279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
D33V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q GAIN MUTATED                                  0     0
  18Q GAIN WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED                           2    48
  18Q GAIN WILD-TYPE                       119   671
D33V13, multiclass
                                  clus
vv                                 18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       2                119
  WHITE                                          48                671
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V14, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     4  32
  18Q GAIN WILD-TYPE  38 590
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      4   32
  18Q GAIN WILD-TYPE   38  590
                        clus
vv                       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               32                590
[1] 2 2
[1] FALSE

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                  0   1
  19P GAIN MUTATED    51  22
  19P GAIN WILD-TYPE 597 206
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                73                803 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                22                206 
$`19P GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-BP-4342 TCGA-BP-5178 TCGA-CZ-4854 TCGA-BQ-5892 
       28.11        38.47        74.17        62.86        46.16        11.97 
TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 
      153.73        98.96        30.25        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       104.55       103.10       105.60 
TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3453 TCGA-B0-4688 
       43.20        18.87       112.08        94.19        83.21         3.32 
TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4822 TCGA-B0-4844 TCGA-B0-5094 
        3.62        57.70        46.59        36.53        10.29        10.95 
TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4166 
       90.87        19.30         5.10         5.46        23.31         0.43 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4994 
       31.89        11.31        13.15         6.74        58.98        43.00 
TCGA-BP-5185 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 
       37.22        19.82        34.95        46.55        79.66        74.27 
TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 
      109.84        49.28       131.08       133.71       122.83        53.42 
TCGA-CW-5591 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 
       74.66       107.41        79.63        90.54        94.45        10.85 
TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 TCGA-BQ-5885 TCGA-G7-A8LC 
       69.96        31.10        67.96         3.91        30.28        23.08 
TCGA-GL-7966 
        3.68 

$`19P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       34.29        31.07        42.97        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       28.73        22.45        19.73        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 
       94.72        32.61         3.58        80.68        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 
       45.07        41.62        27.62        35.90        48.10        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
      103.43         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 
       11.87        19.23        26.04        13.25        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       23.84       109.22       137.06        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.33        96.95        92.55        44.84        86.56        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 
       73.91        71.41        28.80        54.74        44.91       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       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       99.88        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 
       46.78        48.36        78.64        40.01        94.29        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
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-B0-4713 
        1.38        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        40.44        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-B0-4845 
       27.42        53.88         6.71        56.68        10.52        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        37.25        21.21        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       60.30        61.22        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       33.47         0.95       115.00        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       49.25        47.18        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-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-5679 
       18.81        72.00       129.40        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 
       25.25        18.15        62.10        73.35        67.00        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        6.77        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       79.53        23.74        18.44        91.69        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       21.76        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       53.46        12.00        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 
       43.20        47.80        21.63        40.83        26.04        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
       13.08         2.40         1.18         0.43         4.01        51.78 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.43               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            153.73             194.79 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
             43.20              34.49 
[1] "0.4 - 153.7 (43.2)" "0.1 - 194.8 (34.5)"
[1] "hr=" "1"  
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P GAIN MUTATED        21       16        17       20
  19P GAIN WILD-TYPE     433       87       173       84
D34V3, multiclass
           clus
vv          19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                 21                433
  STAGE II                16                 87
  STAGE III               17                173
  STAGE IV                20                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19P GAIN MUTATED    22  16  33   3
  19P GAIN WILD-TYPE 458 111 225  12
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1               22                458
  T2               16                111
  T3               33                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
  19P GAIN MUTATED    35   6   2
  19P GAIN WILD-TYPE 288  38   4
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               35                288
  N1                6                 38
  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  16
  19P GAIN WILD-TYPE 500  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     46   16
  19P GAIN WILD-TYPE  500   73
   clus
vv  19P GAIN MUTATED 19P GAIN WILD-TYPE
  0               46                500
  1               16                 73
[1] 2 2
[1] FALSE
D34V7, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    22  52
  19P GAIN WILD-TYPE 270 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     22   52
  19P GAIN WILD-TYPE  270  538
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               22                270
  MALE                 52                538
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    31   1
  19P GAIN WILD-TYPE 377   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     31    1
  19P GAIN WILD-TYPE  377    2
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                31                377
  YES                1                  2
[1] 2 2
[1] FALSE
D34V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19P GAIN MUTATED                   20                                50
  19P GAIN WILD-TYPE                 46                               478
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19P GAIN MUTATED                                       4
  19P GAIN WILD-TYPE                                   284
D34V10, multiclass
                                       clus
vv                                      19P GAIN MUTATED 19P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  20                 46
  KIDNEY CLEAR CELL RENAL CARCINOMA                   50                478
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                4                284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
D34V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P GAIN MUTATED                                  0     1
  19P GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED                           1    72
  19P GAIN WILD-TYPE                       120   647
D34V13, multiclass
                                  clus
vv                                 19P GAIN MUTATED 19P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       1                120
  WHITE                                          72                647
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V14, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     3  47
  19P GAIN WILD-TYPE  39 575
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      3   47
  19P GAIN WILD-TYPE   39  575
                        clus
vv                       19P GAIN MUTATED 19P GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               47                575
[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 596 203
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                77                799 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                25                203 
$`19Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3336 TCGA-B0-4707 TCGA-BP-4342 TCGA-BP-5178 
       28.11        38.47        34.29        19.73        74.17        62.86 
TCGA-CZ-4854 TCGA-BQ-5892 TCGA-KL-8324 TCGA-KL-8331 TCGA-KL-8336 TCGA-KL-8346 
       46.16        11.97       153.73        98.96        30.25        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
      151.96        49.97        25.91       104.52         3.55        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       104.55       103.10       105.60 
TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3453 
       43.20        18.87       112.08       109.51        94.19        83.21 
TCGA-B0-4688 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4821 TCGA-B0-4822 
        3.32         3.62        57.70        46.59        40.44        36.53 
TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5094 TCGA-B0-5102 TCGA-B0-5109 TCGA-B4-5832 
       10.09        10.29        10.95        90.87        19.30         5.10 
TCGA-B4-5838 TCGA-B8-4143 TCGA-BP-4166 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4768 
        5.46        23.31         0.43        31.89        11.31        13.15 
TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5185 TCGA-BP-5198 
        6.74        58.98        31.30        43.00        37.22        19.82 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4897 TCGA-CJ-4907 
       34.95        46.55        79.66        74.27       109.84        49.28 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CW-5591 TCGA-CZ-4866 
      131.08       133.71       122.83        53.42        74.66       107.41 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5469 
       79.63        90.54        94.45        10.85        69.96        31.10 
TCGA-CZ-5984 TCGA-EU-5905 TCGA-BQ-5885 TCGA-G7-A8LC TCGA-GL-7966 
       67.96         3.91        30.28        23.08         3.68 

$`19Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       31.07        42.97        82.32       109.91        58.49        28.73 
TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       22.45        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 
        3.58        80.68        54.77        12.33        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       27.62        35.90        48.10        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       26.04        13.25        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48       108.62        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-KM-8440 TCGA-KM-8476 TCGA-KM-8477 
       71.41        28.80        54.74        44.91       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-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       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8413 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       99.88        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 
      122.56       109.41        15.78        73.68        68.61        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 
       48.36        78.64        40.01        94.29        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 
       82.45        72.89        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-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 
       65.10         7.82         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         0.59         5.52        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        10.52        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-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.90         7.30        25.32        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        58.59        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         5.75         1.25         0.53 
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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       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-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       62.86        49.08        44.94        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 
       71.41        63.62        58.68        60.30        61.22        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 
       13.41        24.62        33.47         0.95       115.00        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        47.18        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       51.29        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       129.40        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-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       67.00        62.66       119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5458 
       63.42        58.82        79.53        23.74        18.44        91.69 
TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       55.33        10.22        21.76        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
        1.94        12.69        80.19        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 
       22.78        62.63        53.46        12.00        18.12         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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       26.04        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       25.15        20.52        25.84        25.25        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-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.43               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            153.73             194.79 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             43.00              34.49 
[1] "0.4 - 153.7 (43.0)" "0.1 - 194.8 (34.5)"
[1] "hr=" "1.1"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q GAIN MUTATED        22       16        20       20
  19Q GAIN WILD-TYPE     432       87       170       84
D35V3, multiclass
           clus
vv          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                 22                432
  STAGE II                16                 87
  STAGE III               20                170
  STAGE IV                20                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  19Q GAIN MUTATED    23  18  35   2
  19Q GAIN WILD-TYPE 457 109 223  13
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1               23                457
  T2               18                109
  T3               35                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
  19Q GAIN MUTATED    38   5   1
  19Q GAIN WILD-TYPE 285  39   5
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               38                285
  N1                5                 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"
D35V6, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    49  18
  19Q GAIN WILD-TYPE 497  71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     49   18
  19Q GAIN WILD-TYPE  497   71
   clus
vv  19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  0               49                497
  1               18                 71
[1] 2 2
[1] FALSE
D35V7, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    24  54
  19Q GAIN WILD-TYPE 268 536
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     24   54
  19Q GAIN WILD-TYPE  268  536
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               24                268
  MALE                 54                536
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    29   1
  19Q GAIN WILD-TYPE 379   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     29    1
  19Q GAIN WILD-TYPE  379    2
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                29                379
  YES                1                  2
[1] 2 2
[1] FALSE
D35V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19Q GAIN MUTATED                   18                                56
  19Q GAIN WILD-TYPE                 48                               472
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19Q GAIN MUTATED                                       4
  19Q GAIN WILD-TYPE                                   284
D35V10, multiclass
                                       clus
vv                                      19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  18                 48
  KIDNEY CLEAR CELL RENAL CARCINOMA                   56                472
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                4                284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
D35V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q GAIN MUTATED                                  0     1
  19Q GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED                           1    76
  19Q GAIN WILD-TYPE                       120   643
D35V13, multiclass
                                  clus
vv                                 19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       1                120
  WHITE                                          76                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"
D35V14, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     3  52
  19Q GAIN WILD-TYPE  39 570
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      3   52
  19Q GAIN WILD-TYPE   39  570
                        clus
vv                       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               52                570
[1] 2 2
[1] FALSE

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                  0   1
  20P GAIN MUTATED   169  61
  20P GAIN WILD-TYPE 479 167
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               230                646 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                61                167 
$`20P GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3358 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       28.11        38.47        42.97        19.73        43.96        52.21 
TCGA-B8-4621 TCGA-BP-4342 TCGA-BP-4799 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5191 
       25.91        74.17        37.25        35.90        62.86        31.79 
TCGA-CZ-4854 TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       46.16        16.18        22.49         0.89        12.99        76.64 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
       11.97        96.92        48.85        13.61        35.93        14.63 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-KL-8324 
       84.89        17.75        62.83        21.60        15.91       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        98.96        24.79        62.37       151.96        49.97 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 
       25.91       104.52         0.99        52.27        11.21        42.35 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       10.68       100.47       104.55       103.10        99.88       105.60 
TCGA-3Z-A93Z TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3372 
       12.66         0.53        24.16        49.08        37.15        24.16 
TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3433 
       43.20        18.87        65.52       117.80       109.41       112.08 
TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4698 
       94.19        78.64        83.21         3.32         1.41         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4828 
        3.62        65.10        46.59         6.02        36.53        10.09 
TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5106 TCGA-B0-5109 
       40.70        10.29        29.03        10.95        52.54        19.30 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 
       38.63        41.88         5.10         5.46        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4166 TCGA-BP-4167 
       40.04        27.02         0.53         4.93         0.43        89.36 
TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4761 
       64.27         0.07        93.99        62.86        31.89         5.98 
TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4804 
       13.15        68.38        15.78        10.98         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-5010 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5185 TCGA-BP-5198 
       43.00        28.87         2.04        30.64        37.22        19.82 
TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       34.95        46.55        11.05        79.66        47.18        74.27 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4902 
      116.84        66.21        61.91       109.84        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-5682 
       51.29        49.28       131.08       133.71        22.32       122.83 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 
       66.31        74.66         1.35        47.08        69.21         6.77 
TCGA-CZ-4861 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
       14.66       107.41        79.63        94.45        10.85        69.96 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX TCGA-EU-5905 TCGA-2K-A9WE 
        1.94        31.10        67.96        53.46         3.91         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM TCGA-4A-A93W TCGA-4A-A93X 
       75.55         4.57        54.64        30.71         0.13        12.82 
TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       49.58        22.26        78.64        71.80        62.93        19.36 
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
       18.21        19.13        16.64        30.48        25.64        23.97 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-AL-3466 TCGA-AL-3471 
       19.63        19.73        16.31        15.75         9.63        49.32 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 
        2.20        37.51        36.49        20.25        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-5894 TCGA-BQ-7051 TCGA-BQ-7062 
       21.63        25.35         0.95         2.76        50.40         3.81 
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-7130 
       39.25        25.15        17.98        23.08         3.68        58.19 
TCGA-HE-A5NI TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       11.84         2.04        22.26        10.09        18.41        29.10 
TCGA-MH-A55W TCGA-MH-A562 TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-Q2-A5QZ 
       34.29        20.25        17.62         6.61        52.27        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        53.10 
TCGA-UZ-A9PL TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-V9-A7HT 
      103.63        98.96        71.24        47.47       110.73        31.73 
TCGA-WN-AB4C TCGA-Y8-A8S0 
       39.06         6.02 

$`20P GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       34.29        31.07        82.32       109.91        58.49        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       22.45        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      119.38       126.05        24.82         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 
       45.07        41.62        27.62        48.10        49.15        27.02 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-AL-A5DJ 
       25.58        12.26        67.17        61.05        21.37        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       19.23        26.04        13.25        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       11.28       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
        3.02        61.02        17.95        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ 
       29.26        19.73        41.33        86.37        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07        23.84       109.22        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 
       66.54        73.91        71.41        28.80        54.74        44.91 
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-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         3.55        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
       59.08       115.00       100.87       105.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 
       16.67        96.62        90.48        92.55        11.90        36.82 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3430 
        0.10        11.18        10.62        29.10       122.56        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
       73.68        68.61       109.51        46.78        48.36        40.01 
TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        37.58        38.40        82.45        72.89        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        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 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        10.52        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-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
        7.30        25.32        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 
       58.59        66.05        52.73        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
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        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       17.19        23.74         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       17.06         1.74        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 
       90.28       101.06        93.34        99.85        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       62.07        37.25        21.21        15.62        18.48        52.24 
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-4763 TCGA-BP-4765 TCGA-BP-4766 
       12.30        72.59        77.98        41.75        71.80        48.07 
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-4797 TCGA-BP-4801 TCGA-BP-4959 
       60.95        48.95        36.53        36.39        36.95        87.45 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 
       63.62        58.68        60.30        61.22        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4998 
       36.07        33.34        36.95         3.88        46.45        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
       18.51        38.70        37.02        37.48        35.21         6.35 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       79.30        74.20        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 
       13.41        24.62        33.47         0.95       115.00        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17       106.16       114.41        54.61        58.95        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 
       83.97        49.25        75.06        64.27        71.87        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4905 
       50.01        24.66        39.45        50.24        56.35        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       129.40        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
       18.15        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         7.36        64.57        92.02        81.83         5.39 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 
       85.78        73.18        78.18       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
       25.45        58.75        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        90.54        91.69        55.33 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 
       10.22        21.76        84.30        22.52         2.40        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-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         6.77         4.18         7.96        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       59.01        58.22       100.27        56.91        91.73        56.81 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       51.52        38.99        24.33        31.20        29.36         5.29 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA 
       11.57       106.55        90.21        15.48        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        67.43        19.63         0.10        35.18 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
        7.82         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-B1-5398 TCGA-B1-A655 
       70.19        66.71        62.66        67.73        41.13        16.77 
TCGA-B1-A656 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       20.32        29.03        34.49        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.61        43.99        17.23        14.86        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-5889 TCGA-BQ-5890 TCGA-BQ-5893 
       40.83        26.04        30.28        10.82         7.66         7.92 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        93.34        61.28        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5901 
        7.04         7.17        40.77        79.86        74.60        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       24.89        10.68         1.18         0.43        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
       11.05        71.44        20.52        25.84        25.25        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-7129 TCGA-HE-A5NH TCGA-HE-A5NJ 
       12.89        11.21        16.31        81.93        26.01        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A74V 
       96.69        21.34        12.36        12.76        10.55        11.41 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.78        30.38        27.65        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVL TCGA-P4-AAVM 
       87.09        42.94        99.12        92.58        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SR 
       78.90        49.45        44.61        11.93        19.00        26.47 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        18.02        26.20       117.40       125.29        37.35 
TCGA-UZ-A9PQ TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-Y8-A894 
       86.27        30.67        65.13        51.35        26.01        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       18.64        18.05        25.28        13.28 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.10 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            153.73             194.79 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             31.20              36.95 
[1] "0.1 - 153.7 (31.2)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.1"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P GAIN MUTATED        99       31        54       38
  20P GAIN WILD-TYPE     355       72       136       66
D36V3, multiclass
           clus
vv          20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                 99                355
  STAGE II                31                 72
  STAGE III               54                136
  STAGE IV                38                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20P GAIN MUTATED   107  37  81   8
  20P GAIN WILD-TYPE 373  90 177   7
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1              107                373
  T2               37                 90
  T3               81                177
  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    76  16   3
  20P GAIN WILD-TYPE 247  28   3
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               76                247
  N1               16                 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"
D36V6, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   127  30
  20P GAIN WILD-TYPE 419  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    127   30
  20P GAIN WILD-TYPE  419   59
   clus
vv  20P GAIN MUTATED 20P GAIN WILD-TYPE
  0              127                419
  1               30                 59
[1] 2 2
[1] FALSE
D36V7, binary
                    cls
clus                   0   1
  20P GAIN MUTATED    57 176
  20P GAIN WILD-TYPE 235 414
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     57  176
  20P GAIN WILD-TYPE  235  414
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               57                235
  MALE                176                414
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                   0   1
  20P GAIN MUTATED   116   2
  20P GAIN WILD-TYPE 292   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED    116    2
  20P GAIN WILD-TYPE  292    1
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO               116                292
  YES                2                  1
[1] 2 2
[1] FALSE
D36V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20P GAIN MUTATED                   21                               113
  20P GAIN WILD-TYPE                 45                               415
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20P GAIN MUTATED                                      99
  20P GAIN WILD-TYPE                                   189
D36V10, multiclass
                                       clus
vv                                      20P GAIN MUTATED 20P GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  113                415
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               99                189
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
D36V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P GAIN MUTATED                                  0     4
  20P GAIN WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED                          24   197
  20P GAIN WILD-TYPE                        97   522
D36V13, multiclass
                                  clus
vv                                 20P GAIN MUTATED 20P GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                 12
  BLACK OR AFRICAN AMERICAN                      24                 97
  WHITE                                         197                522
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V14, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     8 166
  20P GAIN WILD-TYPE  34 456
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      8  166
  20P GAIN WILD-TYPE   34  456
                        clus
vv                       20P GAIN MUTATED 20P GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 34
  NOT HISPANIC OR LATINO              166                456
[1] 2 2
[1] FALSE

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                  0   1
  20Q GAIN MUTATED   170  64
  20Q GAIN WILD-TYPE 478 164
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               234                642 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                64                164 
$`20Q GAIN MUTATED`
TCGA-KL-8339 TCGA-A3-3325 TCGA-A3-3358 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       28.11        38.47        42.97        19.73        43.96        52.21 
TCGA-B8-4621 TCGA-BP-4342 TCGA-BP-4799 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5191 
       25.91        74.17        37.25        35.90        62.86        31.79 
TCGA-CZ-4854 TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       46.16        16.18        22.49         0.89        12.99        76.64 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7841 
       11.97        96.92        48.85        13.61        35.93        14.63 
TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-KL-8324 
       84.89        17.75        62.83        21.60        15.91       153.73 
TCGA-KL-8327 TCGA-KL-8331 TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        98.96        24.79        62.37       151.96        49.97 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 
       25.91       104.52         0.99        52.27        11.21        42.35 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       10.68       100.47       104.55       103.10        99.88       105.60 
TCGA-3Z-A93Z TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3347 
       12.66         0.53        24.16        49.08        37.15        52.93 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3382 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3429 
       24.16        43.20        18.87        65.52       117.80       109.41 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3453 TCGA-B0-4690 TCGA-B0-4698 
      112.08        94.19        78.64        83.21         1.41         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        3.62        65.10        46.59         6.02        40.44        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        38.63        41.88         5.10         5.46        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4166 
       50.14        40.04        27.02         0.53         4.93         0.43 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4343 TCGA-BP-4351 
       89.36        64.27         0.07        93.99        62.86        31.89 
TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4798 
       11.31         5.98        13.15        68.38        15.78        10.98 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4983 
        6.71        47.97        71.41         6.74        58.98        46.45 
TCGA-BP-4985 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5010 TCGA-BP-5173 TCGA-BP-5175 
       31.30        16.47        43.00        28.87         2.04        30.64 
TCGA-BP-5185 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4635 TCGA-CJ-4644 TCGA-CJ-4871 
       37.22        19.82        34.95        46.55        11.05        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4897 
       47.18        74.27       116.84        66.21        61.91       109.84 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5676 
       47.67        49.97        51.29        49.28       131.08       133.71 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CZ-4857 
       22.32       122.83        66.31        74.66         1.35        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       107.41        79.63        94.45 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-A4VX 
       10.85        69.96         1.94        31.10        67.96        53.46 
TCGA-EU-5905 TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J7 TCGA-2Z-A9JG TCGA-2Z-A9JM 
        3.91         7.04        75.55         4.57        54.64        30.71 
TCGA-4A-A93W TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
        0.13        12.82        49.58        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-7997 
       62.93        19.36        18.21        19.13        16.64        30.48 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A5DU TCGA-A4-A5XZ 
       25.64        23.97        19.63        19.73        16.31        15.75 
TCGA-AL-3466 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
        9.63        49.32         2.20        37.51        36.49        20.25 
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-5894 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DZ-6132 TCGA-DZ-6133 
        0.95         2.76        50.40         3.81        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-7130 TCGA-HE-A5NI TCGA-IA-A40Y 
       17.98        23.08         3.68        58.19        11.84         2.04 
TCGA-IZ-8195 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A562 
       22.26        10.09        18.41        29.10        34.29        20.25 
TCGA-MH-A854 TCGA-P4-A5EA TCGA-P4-AAVK TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       17.62         6.61        52.27        78.90        14.07        47.90 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-UZ-A9PL 
       28.80        27.06        16.31        41.62        53.10       103.63 
TCGA-UZ-A9PP TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A8S0 
       98.96        47.47       110.73        31.73        39.06         6.02 

$`20Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       34.29        31.07        82.32       109.91        58.49        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       22.45        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      119.38       126.05        24.82         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 
      111.02        94.72        32.61         3.58        80.68        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 
       45.07        41.62        27.62        48.10        49.15        27.02 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 
      108.56        53.26       118.85        75.58       103.43         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-AL-A5DJ 
       25.58        12.26        67.17        61.05        21.37        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       19.23        26.04        13.25        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
       11.28       129.86        37.55        24.46        13.78         3.75 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
        3.02        61.02        17.95        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-Y8-A898 TCGA-Y8-A8RZ 
       29.26        19.73        41.33        86.37        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 
       38.07        23.84       109.22        90.48       108.62        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 
       66.54        73.91        71.41        28.80        54.74        44.91 
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-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       25.48        65.19         3.55        87.12        19.33         2.50 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8407 
       59.08       115.00       100.87       105.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E TCGA-A3-3306 
       16.67        96.62        90.48        92.55        11.90        36.82 
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-A3-3346 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01         4.50        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        15.39        22.65         0.10         0.10 
TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
       11.18        10.62        29.10       122.56        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 
       68.61       109.51        46.78        48.36        40.01        94.29 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 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 
       10.52        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-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       25.32        15.09         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 TCGA-B0-5108 
       15.95        62.89        90.87        90.48        30.48        58.59 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       23.74         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F 
       48.53        34.39        14.30        27.29        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
      101.06        93.34        99.85        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-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 
       37.25        21.21        15.62        18.48        52.24        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-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
       77.98        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 
        5.33        61.97        13.51        56.91        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       36.53        36.39        36.95        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       60.30        61.22        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       36.95         3.88        46.45        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       37.02        37.48        35.21         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       33.47         0.95       115.00        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
      114.41        54.61        58.95        21.24        83.97        49.25 
TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       75.06        64.27        71.87        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       39.45        50.24        56.35        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 
      129.40        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4859 
       78.18       105.93        83.90        18.77        25.45        58.75 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       63.39        93.04        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 TCGA-CZ-5463 
       18.44        90.54        91.69        55.33        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       84.30        22.52         2.40        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VZ TCGA-EU-5904 
       12.26        14.63        22.78        62.63        12.00        18.12 
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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.43        19.96        16.37        11.70        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK 
      100.27        56.91        91.73        56.81        51.52        38.99 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93Y TCGA-5P-A9JW 
       24.33        31.20        29.36         5.29        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       90.21        15.48        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7828 TCGA-A4-7915 
       67.43        19.63         0.10        35.18         7.82         0.23 
TCGA-A4-8098 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D 
       29.46        23.28        23.31         0.76        14.33        12.46 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 
       16.96         8.48         8.28        12.46        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3926 
       62.66        67.73        41.13        16.77        20.32        29.03 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-5156 TCGA-B9-A5W8 
       50.50        28.18        26.40        20.61        43.99        17.23 
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-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 
       43.20        47.80        40.83        26.04        30.28        10.82 
TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.66         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 TCGA-DZ-6131 
       49.84         7.63         7.04         7.17        40.77        79.86 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-F9-A97G 
       74.60        34.19        24.89        10.68         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
       51.78        90.90        11.05        71.44        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       25.25        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       85.78        88.24        96.69        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A856 
       10.55        11.41        27.78        30.38        27.65        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SM TCGA-SX-A7SN 
       16.01        50.60        49.45        44.61        11.93        19.00 
TCGA-SX-A7SR TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PM 
       26.47        43.76        18.02        26.20       117.40       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q1 
       37.35        86.27        71.24        30.67        65.13        51.35 
TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S1 
       26.01        18.64        18.64        18.05        25.28        13.28 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.10 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            153.73             194.79 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            31.515             36.950 
[1] "0.1 - 153.7 (31.5)" "0.1 - 194.8 (37.0)"
[1] "hr=" "1.2"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q GAIN MUTATED       100       31        57       38
  20Q GAIN WILD-TYPE     354       72       133       66
D37V3, multiclass
           clus
vv          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                100                354
  STAGE II                31                 72
  STAGE III               57                133
  STAGE IV                38                 66
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  20Q GAIN MUTATED   109  37  84   7
  20Q GAIN WILD-TYPE 371  90 174   8
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1              109                371
  T2               37                 90
  T3               84                174
  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    77  18   3
  20Q GAIN WILD-TYPE 246  26   3
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               77                246
  N1               18                 26
  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"
D37V6, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   131  30
  20Q GAIN WILD-TYPE 415  59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    131   30
  20Q GAIN WILD-TYPE  415   59
   clus
vv  20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  0              131                415
  1               30                 59
[1] 2 2
[1] FALSE
D37V7, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED    60 177
  20Q GAIN WILD-TYPE 232 413
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     60  177
  20Q GAIN WILD-TYPE  232  413
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               60                232
  MALE                177                413
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   116   2
  20Q GAIN WILD-TYPE 292   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    116    2
  20Q GAIN WILD-TYPE  292    1
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO               116                292
  YES                2                  1
[1] 2 2
[1] FALSE
D37V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20Q GAIN MUTATED                   21                               115
  20Q GAIN WILD-TYPE                 45                               413
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20Q GAIN MUTATED                                     101
  20Q GAIN WILD-TYPE                                   187
D37V10, multiclass
                                       clus
vv                                      20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  21                 45
  KIDNEY CLEAR CELL RENAL CARCINOMA                  115                413
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              101                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"
D37V11, continuous
D37V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q GAIN MUTATED                                  0     5
  20Q GAIN WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED                          23   201
  20Q GAIN WILD-TYPE                        98   518
D37V13, multiclass
                                  clus
vv                                 20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           5                 11
  BLACK OR AFRICAN AMERICAN                      23                 98
  WHITE                                         201                518
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V14, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     8 169
  20Q GAIN WILD-TYPE  34 453
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      8  169
  20Q GAIN WILD-TYPE   34  453
                        clus
vv                       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    8                 34
  NOT HISPANIC OR LATINO              169                453
[1] 2 2
[1] FALSE

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                  0   1
  21Q GAIN MUTATED    51  21
  21Q GAIN WILD-TYPE 597 207
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                72                804 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                21                207 
$`21Q GAIN MUTATED`
TCGA-BP-4995 TCGA-BP-5178 TCGA-BP-5191 TCGA-CJ-6027 TCGA-CZ-4854 TCGA-DV-5568 
       45.07        62.86        31.79       118.85        46.16        12.16 
TCGA-DV-5573 TCGA-DV-A4W0 TCGA-2Z-A9JS TCGA-A4-7584 TCGA-B1-A47O TCGA-BQ-5892 
       37.15        81.21        16.18        21.37        27.68        11.97 
TCGA-UZ-A9PZ TCGA-KM-8438 TCGA-KM-8639 TCGA-KN-8433 TCGA-KN-8436 TCGA-A3-3316 
       21.60       151.96        31.33        11.21        42.35        49.08 
TCGA-A3-3322 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3445 TCGA-B0-4690 
       48.59        24.16        18.87       109.41        78.64         1.41 
TCGA-B0-4696 TCGA-B0-4844 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5113 
       28.47        10.29        15.95        90.87        52.54        38.63 
TCGA-B0-5116 TCGA-B0-5696 TCGA-B4-5832 TCGA-B8-5163 TCGA-B8-A54F TCGA-BP-4167 
       41.88        85.78         5.10        27.02        17.06        89.36 
TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4763 
       64.27         0.07        93.99        31.89        11.31        41.75 
TCGA-BP-4781 TCGA-BP-4969 TCGA-BP-4985 TCGA-BP-5173 TCGA-BP-5185 TCGA-CJ-4635 
       68.38        58.98        31.30         2.04        37.22        46.55 
TCGA-CJ-4638 TCGA-CJ-4873 TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CW-5591 TCGA-CZ-4866 
       14.17        74.27       133.71        22.32        74.66       107.41 
TCGA-CZ-5461 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-EU-5905 TCGA-2K-A9WE TCGA-A4-8311 
       10.85         1.94        31.10         3.91         7.04        23.97 
TCGA-A4-8515 TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B9-4117 TCGA-B9-A5W9 TCGA-F9-A8NY 
       23.31        12.46         2.20         0.46         0.16         1.18 
TCGA-G7-A8LC TCGA-HE-A5NJ TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UZ-A9PK TCGA-UZ-A9Q0 
       23.08        56.75         6.61        14.07       117.40       110.73 

$`21Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       25.81        27.22         5.82        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       48.10        49.15        27.02        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6030 
      105.37        26.93        27.65       108.56        53.26        75.58 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
      103.43         0.59       107.54         5.46        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-G6-A8L7 
       65.88        11.67        66.28        56.84        23.90        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7734 TCGA-A4-A5Y1 
       22.49        12.26        67.17        61.05         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        49.25        21.67        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 
       11.87        19.23        26.04        13.25        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       86.37        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       54.74        62.37        44.91        49.97       123.12        51.06 
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-8434 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
        2.50        59.08       115.00       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       99.88       105.60        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       11.90        36.82         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
       37.15        49.58        36.36        38.99        37.38        48.82 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       46.78        48.36        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        5.52        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        10.52        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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5107 
        2.24        21.86        52.08        62.89        90.48        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       58.59        19.30        66.05        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
      129.67        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.75         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G 
        0.53        34.39        14.30        27.29        29.88         1.74 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        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-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       62.07        37.25        21.21        15.62        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       62.86        49.08        44.94        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
       12.30        72.59        77.98         5.98        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       13.15        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       56.91        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
      115.00        73.22       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
       18.81       131.08        72.00       129.40        25.71        18.87 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       90.54        91.69        55.33        94.45        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 
       69.96        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       53.46        12.00        18.12         6.77         4.18         7.96 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
       11.70        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8516 TCGA-A4-8517 
       30.48        29.46        25.64        23.28         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-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
       15.75         8.28         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       62.66        67.73        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 
       12.46        50.50        28.18        26.40        20.61         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK 
       16.31        81.93        58.19        26.01        11.84        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL 
       26.47        53.10        43.76        18.02        26.20       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       47.47        65.13        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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 
            31.200             36.375 
[1] "0.1 - 152.0 (31.2)" "0.1 - 194.8 (36.4)"
[1] "hr=" "1.2"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q GAIN MUTATED        34        6        21        9
  21Q GAIN WILD-TYPE     420       97       169       95
D38V3, multiclass
           clus
vv          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                 34                420
  STAGE II                 6                 97
  STAGE III               21                169
  STAGE IV                 9                 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
  21Q GAIN MUTATED    36   7  27   2
  21Q GAIN WILD-TYPE 444 120 231  13
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1               36                444
  T2                7                120
  T3               27                231
  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 300  41   6
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0               23                300
  N1                3                 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"
D38V6, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    42   9
  21Q GAIN WILD-TYPE 504  80
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     42    9
  21Q GAIN WILD-TYPE  504   80
   clus
vv  21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  0               42                504
  1                9                 80
[1] 2 2
[1] FALSE
D38V7, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    22  50
  21Q GAIN WILD-TYPE 270 540
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     22   50
  21Q GAIN WILD-TYPE  270  540
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               22                270
  MALE                 50                540
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    30   0
  21Q GAIN WILD-TYPE 378   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     30    0
  21Q GAIN WILD-TYPE  378    3
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                30                378
  YES                0                  3
[1] 2 2
[1] FALSE
D38V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  21Q GAIN MUTATED                    4                                49
  21Q GAIN WILD-TYPE                 62                               479
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  21Q GAIN MUTATED                                      19
  21Q GAIN WILD-TYPE                                   269
D38V10, multiclass
                                       clus
vv                                      21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                   49                479
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               19                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"
D38V11, continuous
D38V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q GAIN MUTATED                                  1     1
  21Q GAIN WILD-TYPE                                1    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED                           5    64
  21Q GAIN WILD-TYPE                       116   655
D38V13, multiclass
                                  clus
vv                                 21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                1                  1
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       5                116
  WHITE                                          64                655
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V14, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     4  51
  21Q GAIN WILD-TYPE  38 571
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      4   51
  21Q GAIN WILD-TYPE   38  571
                        clus
vv                       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               51                571
[1] 2 2
[1] FALSE

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED    47  16
  22Q GAIN WILD-TYPE 601 212
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                63                813 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                16                212 
$`22Q GAIN MUTATED`
TCGA-BP-4342 TCGA-BP-5178 TCGA-BQ-5892 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 
       74.17        62.86        11.97        38.07       153.73       137.06 
TCGA-KL-8341 TCGA-KL-8346 TCGA-KM-8443 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 
       24.79        62.37        49.97        23.47        25.91         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KO-8405 TCGA-KO-8408 
        0.99        52.27        11.21        42.35       100.47        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-A3-3306 TCGA-A3-3319 
      104.55       103.10        99.88       105.60        36.82        37.15 
TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 TCGA-AK-3440 TCGA-B0-4688 TCGA-B0-4699 
       43.20        18.87       112.08        94.19         3.32         3.62 
TCGA-B0-5081 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5113 TCGA-B0-5400 TCGA-B4-5832 
       11.90        15.95        90.87        38.63        56.98         5.10 
TCGA-B4-5838 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4337 TCGA-BP-4351 
        5.46         0.43        61.78        64.27         0.07        31.89 
TCGA-BP-4352 TCGA-BP-4765 TCGA-BP-4781 TCGA-BP-4975 TCGA-BP-4994 TCGA-BP-5173 
       11.31        71.80        68.38        47.11        43.00         2.04 
TCGA-BP-5185 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5671 
       37.22        19.82        34.95        51.29        49.28       131.08 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CW-5588 TCGA-CW-5591 TCGA-CZ-4860 TCGA-CZ-5984 
      133.71       122.83        66.31        74.66         6.77        67.96 
TCGA-5P-A9K9 TCGA-G7-A8LB TCGA-V9-A7HT 
       19.36        17.98        31.73 

$`22Q GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 
       48.10        49.15        27.02        31.79        44.55        31.27 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       63.25       105.37        26.93        27.65       108.56        53.26 
TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
      118.85        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       13.25        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 
       15.62         6.74        23.84       109.22        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       44.84        86.56        66.54        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       54.74       151.96        44.91       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       105.47 
TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       10.68       103.40        92.71        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       12.66        11.90         0.53        39.16        24.16        49.08 
TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       49.02        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
       19.00         1.38        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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24         7.30        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5104 
        8.05         2.24        21.86        52.08        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 
       52.54        30.48        58.59        19.30        66.05        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         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        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 
       42.71        25.05        45.37        17.19        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        48.53         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4177 
       99.85        89.36        23.05        77.03        62.24        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        27.78        62.07        37.25        21.21 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       15.62        93.99        18.48        52.24        62.86        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-4761 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       77.98         5.98        41.75        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
       10.82         5.33        61.97        13.51        56.91        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4977 TCGA-BP-4981 
       48.89        49.38        45.50         6.94        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       33.47         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       47.67        49.97        49.18        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06         4.57        18.81        72.00       129.40 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
       25.71        18.87        22.32        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
       64.57        92.02        81.83         5.39        85.78        73.18 
TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 
       78.18         1.35       105.93        83.90        18.77        25.45 
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-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        31.10        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       51.35        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              0.07               0.10 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            153.73             194.79 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             42.35              34.49 
[1] "0.1 - 153.7 (42.4)" "0.1 - 194.8 (34.5)"
[1] "hr=" "1.2"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q GAIN MUTATED        23       13        15       12
  22Q GAIN WILD-TYPE     431       90       175       92
D39V3, multiclass
           clus
vv          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                 23                431
  STAGE II                13                 90
  STAGE III               15                175
  STAGE IV                12                 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
  22Q GAIN MUTATED    23  14  23   4
  22Q GAIN WILD-TYPE 457 113 235  11
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1               23                457
  T2               14                113
  T3               23                235
  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   2
  22Q GAIN WILD-TYPE 293  41   4
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0               30                293
  N1                3                 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"
D39V6, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    44   8
  22Q GAIN WILD-TYPE 502  81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     44    8
  22Q GAIN WILD-TYPE  502   81
   clus
vv  22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  0               44                502
  1                8                 81
[1] 2 2
[1] FALSE
D39V7, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    18  46
  22Q GAIN WILD-TYPE 274 544
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     18   46
  22Q GAIN WILD-TYPE  274  544
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               18                274
  MALE                 46                544
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED    30   1
  22Q GAIN WILD-TYPE 378   2
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     30    1
  22Q GAIN WILD-TYPE  378    2
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                30                378
  YES                1                  2
[1] 2 2
[1] FALSE
D39V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  22Q GAIN MUTATED                   19                                40
  22Q GAIN WILD-TYPE                 47                               488
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  22Q GAIN MUTATED                                       5
  22Q GAIN WILD-TYPE                                   283
D39V10, multiclass
                                       clus
vv                                      22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  19                 47
  KIDNEY CLEAR CELL RENAL CARCINOMA                   40                488
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                5                283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
D39V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q GAIN MUTATED                                  0     1
  22Q GAIN WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED                           3    60
  22Q GAIN WILD-TYPE                       118   659
D39V13, multiclass
                                  clus
vv                                 22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       3                118
  WHITE                                          60                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"
D39V14, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     4  35
  22Q GAIN WILD-TYPE  38 587
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4   35
  22Q GAIN WILD-TYPE   38  587
                        clus
vv                       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               35                587
[1] 2 2
[1] FALSE

Clustering(40) Variable = XP GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XP GAIN MUTATED   103  24
  XP GAIN WILD-TYPE 545 204
  XP GAIN MUTATED XP GAIN WILD-TYPE 
              127               749 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
               24               204 
$`XP GAIN MUTATED`
TCGA-BP-4799 TCGA-CZ-4854 TCGA-2Z-A9JQ TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A657 
       37.25        46.16        25.58        76.64        21.67        21.07 
TCGA-B3-A6W5 TCGA-BQ-7046 TCGA-DW-5561 TCGA-DW-7836 TCGA-GL-A59T TCGA-HE-A5NF 
       10.16        96.92        13.61        35.93        17.95        84.89 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-Y8-A895 TCGA-KL-8346 TCGA-KN-8419 TCGA-KN-8423 
       17.75        62.83        15.91        62.37        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-A3-3346 
        3.55        11.21       103.10        99.88       105.60         4.50 
TCGA-A3-3382 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3453 
       18.87       122.56       109.41       109.51        78.64        83.21 
TCGA-B0-4827 TCGA-B0-5080 TCGA-B0-5109 TCGA-B8-A54D TCGA-B8-A54I TCGA-BP-4162 
       29.10        11.24        19.30        27.29         4.93       101.06 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4770 
       61.78         0.07        93.99        11.31        12.30        10.82 
TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 
       58.98         3.88        11.05       113.46        50.24        18.15 
TCGA-CW-5591 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-DV-A4VX TCGA-EU-5905 
       74.66        79.63        69.96         1.94        53.46         3.91 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY 
       75.55        59.01        58.22       100.27        56.91        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-A4-8311 TCGA-A4-8515 
       22.26        78.64        71.80        62.93        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
        0.76        19.63        14.33        16.96        16.31        15.75 
TCGA-A4-A6HP TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B3-4103 TCGA-B9-4113 
       12.46        49.32         2.20        36.49        30.58        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-7060 
       47.80        25.35         0.95         7.92        48.26         7.04 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        3.81        40.77        51.19         2.40         1.18        51.78 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-HE-7129 TCGA-HE-A5NI 
       39.25        25.25        17.98       194.79        81.93        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       56.75        25.22        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL TCGA-SX-A71U 
       27.78        87.09        99.12        52.27        16.01        44.61 
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        53.10 
TCGA-UZ-A9PK TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
      117.40        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT 
       31.73 

$`XP GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       11.64        20.38         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JS 
       23.01        75.42        34.85        39.88        33.07        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       12.99        49.25        27.68        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       26.04        13.25        11.97        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       11.28        48.85       129.86        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 
        3.75        14.63         3.02        61.02        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       12.13        29.26        19.73        41.33        86.37        21.60 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 
       24.79        73.91        71.41        28.80        54.74       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
       87.91        25.48        65.19       104.52         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-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       16.67       104.55        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       11.90        36.82         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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
      117.80        15.78        73.68       112.08        68.61        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 
       46.78        48.36        40.01        94.29        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F 
       48.53         0.53        34.39        14.30        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       62.07        37.25        21.21        15.62        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       62.86        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       31.33        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        13.15        61.68         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
       36.95        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17       106.16       114.41        54.61        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 
      116.84        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-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45       109.84        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40        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-A4VZ 
       65.65        12.26        14.63        22.78        62.63        12.00 
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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 
       12.82        11.57       106.55        90.21        15.48        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 
       16.64        30.48        29.46        25.64        23.28        19.73 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       12.46         8.48         8.28         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 
       62.66        67.73        41.13        37.51        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
       20.32        33.83        29.03        34.49        12.46        26.40 
TCGA-B9-4116 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
       20.61        22.06        17.23        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-5889 TCGA-BQ-5890 TCGA-BQ-5894 
       40.83        26.04        30.28        10.82         7.66         2.76 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        7.17        79.86        80.88        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 
       24.89        10.68        13.08         0.43         4.01        90.90 
TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
       11.05        71.44        25.15        20.52        25.84        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       16.90        80.65        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        58.19        26.01 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       73.25        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       10.09        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM 
       15.48        99.78        42.94         6.61        92.58        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM 
       78.90        14.07        47.90        49.45        27.06        11.93 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        18.02        26.20       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
       98.96        86.27        71.24        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  XP GAIN MUTATED XP GAIN WILD-TYPE 
             0.07              0.10 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
           194.79            153.73 
  XP GAIN MUTATED XP GAIN WILD-TYPE 
            29.10             36.53 
[1] "0.1 - 194.8 (29.1)" "0.1 - 153.7 (36.5)"
[1] "hr=" "1.4"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP GAIN MUTATED        74       14        15       16
  XP GAIN WILD-TYPE     380       89       175       88
D40V3, multiclass
           clus
vv          XP GAIN MUTATED XP GAIN WILD-TYPE
  STAGE I                74               380
  STAGE II               14                89
  STAGE III              15               175
  STAGE IV               16                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
  XP GAIN MUTATED    81  19  26   3
  XP GAIN WILD-TYPE 399 108 232  12
D40V4, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  T1              81               399
  T2              19               108
  T3              26               232
  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    37   5   0
  XP GAIN WILD-TYPE 286  39   6
D40V5, multiclass
    clus
vv   XP GAIN MUTATED XP GAIN WILD-TYPE
  N0              37               286
  N1               5                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    51  12
  XP GAIN WILD-TYPE 495  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     51   12
  XP GAIN WILD-TYPE  495   77
   clus
vv  XP GAIN MUTATED XP GAIN WILD-TYPE
  0              51               495
  1              12                77
[1] 2 2
[1] FALSE
D40V7, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    29 100
  XP GAIN WILD-TYPE 263 490
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     29  100
  XP GAIN WILD-TYPE  263  490
        clus
vv       XP GAIN MUTATED XP GAIN WILD-TYPE
  FEMALE              29               263
  MALE               100               490
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XP GAIN MUTATED    81   0
  XP GAIN WILD-TYPE 327   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED     81    0
  XP GAIN WILD-TYPE  327    3
     clus
vv    XP GAIN MUTATED XP GAIN WILD-TYPE
  NO               81               327
  YES               0                 3
[1] 2 2
[1] FALSE
D40V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XP GAIN MUTATED                    8                                33
  XP GAIN WILD-TYPE                 58                               495
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XP GAIN MUTATED                                      88
  XP GAIN WILD-TYPE                                   200
D40V10, multiclass
                                       clus
vv                                      XP GAIN MUTATED XP GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                  33               495
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              88               200
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
D40V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP GAIN MUTATED                                  2     3
  XP GAIN WILD-TYPE                                0    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP GAIN MUTATED                          19    99
  XP GAIN WILD-TYPE                       102   620
D40V13, multiclass
                                  clus
vv                                 XP GAIN MUTATED XP GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                     19               102
  WHITE                                         99               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"
D40V14, binary
                   cls
clus                  0   1
  XP GAIN MUTATED     5  99
  XP GAIN WILD-TYPE  37 523
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP GAIN MUTATED      5   99
  XP GAIN WILD-TYPE   37  523
                        clus
vv                       XP GAIN MUTATED XP GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                37
  NOT HISPANIC OR LATINO              99               523
[1] 2 2
[1] FALSE

Clustering(41) Variable = XQ GAIN MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED   105  23
  XQ GAIN WILD-TYPE 543 205
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
              128               748 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               23               205 
$`XQ GAIN MUTATED`
TCGA-BP-4799 TCGA-CZ-4854 TCGA-MM-A84U TCGA-2Z-A9JQ TCGA-AL-3468 TCGA-B1-A47M 
       37.25        46.16        23.01        25.58        76.64        21.67 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A44B TCGA-BQ-7046 TCGA-DW-5561 TCGA-DW-7836 
       21.07        10.16        11.87        96.92        13.61        35.93 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-Y8-A895 TCGA-KL-8346 
       17.95        84.89        17.75        62.83        15.91        62.37 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KO-8410 TCGA-KO-8413 
       23.47        25.91         3.55        11.21       103.10        99.88 
TCGA-KO-8414 TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 
      105.60        28.31       122.56       109.41       109.51        83.21 
TCGA-B0-4827 TCGA-B0-5080 TCGA-B0-5109 TCGA-B8-A54D TCGA-B8-A54I TCGA-BP-4162 
       29.10        11.24        19.30        27.29         4.93       101.06 
TCGA-BP-4174 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4352 TCGA-BP-4969 TCGA-BP-4989 
       61.78         0.07        93.99        11.31        58.98         3.88 
TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 TCGA-CW-5591 
       52.27        11.05       113.46        50.24        18.15        74.66 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-DV-A4VX TCGA-EU-5905 
       79.63        91.69        69.96         1.94        53.46         3.91 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-5P-A9JY 
       75.55        59.01        58.22       100.27        56.91        49.58 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-A4-8311 TCGA-A4-8515 
       22.26        78.64        71.80        62.93        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ 
        0.76        19.63        14.33        16.96        16.31        15.75 
TCGA-A4-A6HP TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B3-4103 TCGA-B9-4113 
       12.46        49.32         2.20        36.49        30.58        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-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6133 TCGA-F9-A7VF TCGA-F9-A8NY 
        7.04         3.81        40.77        51.19         2.40         1.18 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-GL-6846 TCGA-HE-7129 
       51.78        39.25        25.25        17.98       194.79        81.93 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       11.84        56.75        25.22        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVL 
       34.29        27.78        87.09        99.12        52.27        16.01 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       44.61        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       53.10       117.40        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       51.35        31.73 

$`XQ GAIN WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       11.64        20.38         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        39.88        33.07        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-A5DJ TCGA-B1-A47O TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       49.25        27.68        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       11.97        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
      129.86        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
        3.02        61.02        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A898 TCGA-Y8-A8RZ 
       19.73        41.33        86.37        21.60        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       71.41        28.80        54.74       151.96        44.91        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-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
        2.50        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       96.62        90.48        92.55        12.66        11.90        36.82 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        65.52        20.28        33.47        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       117.80 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 
       48.36        78.64        40.01        94.29        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
       90.48        52.54        30.48        58.59        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54E TCGA-B8-A54F 
       48.53         0.53        34.39        14.30        29.88        17.06 
TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4340 TCGA-BP-4341 
       62.07        37.25        21.21        15.62        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       62.86        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4787 
       61.97        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 
       46.45        31.30        36.95        46.45        16.47        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4900 TCGA-CJ-4901 
       50.01        24.66        39.45       109.84        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       25.25       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 
        5.39        85.78        73.18        66.31        78.18         1.35 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       58.75         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82        79.53        23.74        18.44        90.54 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        94.45        10.85        10.22        21.76        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40        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-A4VZ 
       65.65        12.26        14.63        22.78        62.63        12.00 
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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K3 TCGA-5P-A9K8 
       12.82        11.57       106.55        90.21        15.48        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8518 
       16.64        30.48        29.46        25.64        23.28        19.73 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3472 
       12.46         8.48         8.28         9.63        70.19        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A654 TCGA-B1-A655 
       62.66        67.73        41.13        37.51        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4115 
       20.32        33.83        29.03        34.49        12.46        26.40 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
       22.06        17.23        14.86        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 
       26.04        30.28        10.82         7.66         2.76       123.62 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7061 
       93.34        61.28        50.40        49.84         7.63         7.17 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       79.86        80.88        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6793 
       10.68        13.08         0.43         4.01        90.90        11.05 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD 
       71.44        25.15        20.52        25.84        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
       80.65        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NK 
       12.89        11.21        16.31        58.19        26.01        73.25 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVM TCGA-P4-AAVO 
       99.78        42.94         6.61        92.58        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SU 
       14.07        47.90        49.45        27.06        11.93        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       18.02        26.20       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       86.27        71.24        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.07              0.10 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
           194.79            153.73 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            29.84             36.46 
[1] "0.1 - 194.8 (29.8)" "0.1 - 153.7 (36.5)"
[1] "hr=" "1.5"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ GAIN MUTATED        74       14        16       15
  XQ GAIN WILD-TYPE     380       89       174       89
D41V3, multiclass
           clus
vv          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                74               380
  STAGE II               14                89
  STAGE III              16               174
  STAGE IV               15                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
  XQ GAIN MUTATED    81  20  27   2
  XQ GAIN WILD-TYPE 399 107 231  13
D41V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1              81               399
  T2              20               107
  T3              27               231
  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    35   5   0
  XQ GAIN WILD-TYPE 288  39   6
D41V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              35               288
  N1               5                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    49  12
  XQ GAIN WILD-TYPE 497  77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     49   12
  XQ GAIN WILD-TYPE  497   77
   clus
vv  XQ GAIN MUTATED XQ GAIN WILD-TYPE
  0              49               497
  1              12                77
[1] 2 2
[1] FALSE
D41V7, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    30 100
  XQ GAIN WILD-TYPE 262 490
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     30  100
  XQ GAIN WILD-TYPE  262  490
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              30               262
  MALE               100               490
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    81   0
  XQ GAIN WILD-TYPE 327   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     81    0
  XQ GAIN WILD-TYPE  327    3
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO               81               327
  YES               0                 3
[1] 2 2
[1] FALSE
D41V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XQ GAIN MUTATED                    8                                32
  XQ GAIN WILD-TYPE                 58                               496
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XQ GAIN MUTATED                                      90
  XQ GAIN WILD-TYPE                                   198
D41V10, multiclass
                                       clus
vv                                      XQ GAIN MUTATED XQ GAIN WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                  32               496
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              90               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"
D41V11, continuous
D41V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ GAIN MUTATED                                  2     2
  XQ GAIN WILD-TYPE                                0    14
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED                          22    98
  XQ GAIN WILD-TYPE                        99   621
D41V13, multiclass
                                  clus
vv                                 XQ GAIN MUTATED XQ GAIN WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               2                 0
  ASIAN                                          2                14
  BLACK OR AFRICAN AMERICAN                     22                99
  WHITE                                         98               621
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V14, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     5 101
  XQ GAIN WILD-TYPE  37 521
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      5  101
  XQ GAIN WILD-TYPE   37  521
                        clus
vv                       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  HISPANIC OR LATINO                   5                37
  NOT HISPANIC OR LATINO             101               521
[1] 2 2
[1] FALSE

Clustering(42) Variable = 1P LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                 0   1
  1P LOSS MUTATED   108  36
  1P LOSS WILD-TYPE 540 192
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
              144               732 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               36               192 
$`1P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-4342 TCGA-BP-4353 
      102.81        28.11        47.24       130.13        74.17        12.33 
TCGA-BP-4775 TCGA-BP-4986 TCGA-BP-5201 TCGA-CJ-4894 TCGA-BQ-7055 TCGA-PJ-A5Z8 
       60.59        25.81        31.27        27.65        26.27        19.73 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       49.97       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
      104.52         0.99        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       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       104.55       105.60        96.62        90.48        92.55 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 
       24.16        49.08        53.29        43.20        18.64       117.80 
TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4698 
      112.08        94.19        40.01        12.13        40.70         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-B0-5098 TCGA-B0-5102 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 
        7.30        52.08        90.87        52.87        42.41        73.84 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 
       32.61         1.68         0.53         5.46        17.19         6.38 
TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4968 TCGA-BP-4994 
       64.27        21.21        13.15        68.38        57.40        43.00 
TCGA-BP-5004 TCGA-BP-5173 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4897 
       37.02         2.04        46.55       114.41        64.27       109.84 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5678 TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 
       47.67        49.28        18.87        66.31         6.77       107.41 
TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5469 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-T7-A92I 
       90.54        10.22        31.10         4.18        35.87        11.70 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K3 TCGA-5P-A9K8 
       54.64        51.52        12.82        49.58        15.48        43.04 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-B1-7332 TCGA-B3-3926 
       67.43        18.21         0.10        29.46        37.51        29.03 
TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-F9-A4JJ 
       17.23        86.76        21.63         2.76       123.62        10.68 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 
       13.08         4.01        25.15        25.84        23.08        27.65 
TCGA-HE-A5NK TCGA-IA-A40Y TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       73.25         2.04         6.61        14.07        18.02        86.27 

$`1P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 
        3.58        80.68        54.77        77.62        44.15        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 
       20.38        37.25         6.94        61.51        53.65        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 
       62.86        49.15        27.02        31.79        44.55        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
      105.37        26.93       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      103.43        46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       96.92        44.84        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       16.34        12.13        29.26        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KM-8477 
       86.37        21.60        15.91        15.62         6.74        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8433 
       31.33        23.47        25.91         3.55        52.27        11.21 
TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
      100.87        10.68       103.10        99.88        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       36.82         0.53        39.16        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        62.01 
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-A3-3362 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-A3-3376 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       10.62        29.10       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 
       68.61       109.51        46.78        48.36        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       83.21        37.58        38.40        82.45        72.89         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-B0-4710 
       19.00        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 
        5.52        45.07        33.50        16.77         6.02        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
       27.42        53.88         6.71        56.68        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        8.05         2.24        21.86        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        71.41       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
      131.15        89.49        91.46        35.90        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
        5.75         5.10         1.25         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        49.97        42.71        25.05        45.37 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       24.23        50.14        16.60        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 
       62.24        61.78        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 
        5.98        41.75        71.80        48.07        61.68        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        58.98        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       30.64        18.51        38.70        37.48        35.21        28.87 
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-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82        34.95         0.95       115.00        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       39.45        50.24        56.35        49.97        51.29        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       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
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-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        94.45        10.85        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       53.46        12.00        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-2K-A9WE 
       10.29         2.01        19.43        19.96        16.37         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ 
       29.36         5.29         0.13        11.57       106.55        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA 
       22.26        78.64        71.80        62.93        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       12.39        27.09        19.63        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
        0.23        16.64        30.48        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
        2.20        41.13        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       33.83        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        14.86        17.49        12.30        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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       51.19        74.60        34.19        19.00        24.89         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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       71.44        20.52        25.25        17.98        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
      194.79        12.92         3.68         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       56.75        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.10              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           153.73            194.79 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           44.875            33.470 
[1] "0.1 - 153.7 (44.9)" "0.1 - 194.8 (33.5)"
[1] "hr=" "1.3"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1P LOSS MUTATED        56       34        32       17
  1P LOSS WILD-TYPE     398       69       158       87
D42V3, multiclass
           clus
vv          1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                56               398
  STAGE II               34                69
  STAGE III              32               158
  STAGE IV               17                87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P LOSS MUTATED    60  38  42   5
  1P LOSS WILD-TYPE 420  89 216  10
D42V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1              60               420
  T2              38                89
  T3              42               216
  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  10   3
  1P LOSS WILD-TYPE 259  34   3
D42V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              64               259
  N1              10                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"
D42V6, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    93   9
  1P LOSS WILD-TYPE 453  80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     93    9
  1P LOSS WILD-TYPE  453   80
   clus
vv  1P LOSS MUTATED 1P LOSS WILD-TYPE
  0              93               453
  1               9                80
[1] 2 2
[1] FALSE
D42V7, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    52  93
  1P LOSS WILD-TYPE 240 497
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     52   93
  1P LOSS WILD-TYPE  240  497
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              52               240
  MALE                93               497
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    92   0
  1P LOSS WILD-TYPE 316   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     92    0
  1P LOSS WILD-TYPE  316    3
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO               92               316
  YES               0                 3
[1] 2 2
[1] FALSE
D42V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1P LOSS MUTATED                   53                                60
  1P LOSS WILD-TYPE                 13                               468
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1P LOSS MUTATED                                      32
  1P LOSS WILD-TYPE                                   256
D42V10, multiclass
                                       clus
vv                                      1P LOSS MUTATED 1P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 53                13
  KIDNEY CLEAR CELL RENAL CARCINOMA                  60               468
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              32               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"
D42V11, continuous
D42V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1P LOSS MUTATED                                  0     4
  1P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED                          19   116
  1P LOSS WILD-TYPE                       102   603
D42V13, multiclass
                                  clus
vv                                 1P LOSS MUTATED 1P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     19               102
  WHITE                                        116               603
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V14, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    10  86
  1P LOSS WILD-TYPE  32 536
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     10   86
  1P LOSS WILD-TYPE   32  536
                        clus
vv                       1P LOSS MUTATED 1P LOSS WILD-TYPE
  HISPANIC OR LATINO                  10                32
  NOT HISPANIC OR LATINO              86               536
[1] 2 2
[1] FALSE

Clustering(43) Variable = 1Q LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                 0   1
  1Q LOSS MUTATED    85  24
  1Q LOSS WILD-TYPE 563 204
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
              109               767 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               204 
$`1Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-4353 TCGA-BP-4775 
      102.81        28.11        47.24       130.13        12.33        60.59 
TCGA-BP-4986 TCGA-PJ-A5Z8 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 
       25.81        19.73        38.07       153.73        23.84       137.06 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        49.97       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         0.99        52.27        87.12        19.33 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 
       59.08       115.00        42.35       105.47       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       104.55       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 
       92.55        43.20        18.64       117.80       112.08        94.19 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4821 
       12.13        40.70        28.47         1.38         3.62        40.44 
TCGA-B0-4834 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5102 TCGA-B0-5117 TCGA-B2-3923 
       68.71        65.29        36.85        90.87        52.87        32.61 
TCGA-B2-4098 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4334 TCGA-BP-4768 
        1.68         5.46        17.19         6.38        21.21        13.15 
TCGA-BP-4968 TCGA-BP-4994 TCGA-CJ-4876 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 
       57.40        43.00        64.27       109.84        47.67        49.28 
TCGA-CW-5588 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-G6-A8L8 
       66.31         6.77       107.41        90.54        31.10        35.87 
TCGA-2Z-A9JG TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       54.64        12.82        49.58        67.43        18.21         0.10 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5894 TCGA-F9-A7Q0 
       37.51        16.77        29.03        17.23         2.76        13.08 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-8500 TCGA-HE-A5NK TCGA-P4-A5EA 
       25.15        25.84        23.08        27.65        73.25         6.61 
TCGA-UN-AAZ9 
       18.02 

$`1Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
        3.58        80.68        74.17        54.77        77.62        44.15 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       29.26        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KM-8477 TCGA-KM-8639 
       15.91        15.62         6.74       109.22        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8437 
       23.47        25.91         3.55         2.50        11.21       100.87 
TCGA-KO-8404 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       10.68       103.10        99.88        12.66        11.90        36.82 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
       24.16        53.29        55.76        20.71        18.87        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        15.39        22.65         0.10 
TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3428 TCGA-AK-3429 
        0.10        11.18        10.62        29.10       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
       82.45        72.89         1.41         3.32         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        2.53         3.48        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        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       56.68        10.52        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-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 
       21.86        52.08        15.95        62.89        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 
       79.89       131.15        89.49        91.46        35.90        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       25.05        45.37        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
       27.02         0.85        24.23        50.14        16.60        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
       90.28       101.06        93.34        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
       23.05        77.03        62.24        61.78        64.27        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
       97.45        53.42        27.78        62.07        37.25        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 
       36.95         3.88        46.45        16.47        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06       116.84        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 
       50.01        24.66        39.45        50.24        56.35        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       51.29        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       91.73        56.81        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW 
       31.20        29.36         5.29         0.13        11.57       106.55 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 
       43.04        19.36        12.99        12.39        27.09        19.63 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       36.49        20.25        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        1.15        43.99        22.06         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 
       25.35        10.82         7.66         0.95         7.92       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
       11.05        39.25        71.44        20.52        25.25        17.98 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
       16.90        80.65       194.79        12.92         3.68         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       26.01        11.84        56.75        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.10              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           153.73            194.79 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            49.58             33.47 
[1] "0.1 - 153.7 (49.6)" "0.1 - 194.8 (33.5)"
[1] "hr=" "1.6"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  1Q LOSS MUTATED        44       30        21       11
  1Q LOSS WILD-TYPE     410       73       169       93
D43V3, multiclass
           clus
vv          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                44               410
  STAGE II               30                73
  STAGE III              21               169
  STAGE IV               11                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
  1Q LOSS MUTATED    47  31  28   4
  1Q LOSS WILD-TYPE 433  96 230  11
D43V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1              47               433
  T2              31                96
  T3              28               230
  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    56   7   2
  1Q LOSS WILD-TYPE 267  37   4
D43V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              56               267
  N1               7                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"
D43V6, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    72   5
  1Q LOSS WILD-TYPE 474  84
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     72    5
  1Q LOSS WILD-TYPE  474   84
   clus
vv  1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  0              72               474
  1               5                84
[1] 2 2
[1] FALSE
D43V7, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    42  68
  1Q LOSS WILD-TYPE 250 522
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     42   68
  1Q LOSS WILD-TYPE  250  522
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              42               250
  MALE                68               522
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    78   0
  1Q LOSS WILD-TYPE 330   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     78    0
  1Q LOSS WILD-TYPE  330    3
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO               78               330
  YES               0                 3
[1] 2 2
[1] FALSE
D43V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  1Q LOSS MUTATED                   52                                38
  1Q LOSS WILD-TYPE                 14                               490
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  1Q LOSS MUTATED                                      20
  1Q LOSS WILD-TYPE                                   268
D43V10, multiclass
                                       clus
vv                                      1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 52                14
  KIDNEY CLEAR CELL RENAL CARCINOMA                  38               490
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              20               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"
D43V11, continuous
D43V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  1Q LOSS MUTATED                                  0     4
  1Q LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED                          11    90
  1Q LOSS WILD-TYPE                       110   629
D43V13, multiclass
                                  clus
vv                                 1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     11               110
  WHITE                                         90               629
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V14, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     8  67
  1Q LOSS WILD-TYPE  34 555
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      8   67
  1Q LOSS WILD-TYPE   34  555
                        clus
vv                       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                34
  NOT HISPANIC OR LATINO              67               555
[1] 2 2
[1] FALSE

Clustering(44) Variable = 2P LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                 0   1
  2P LOSS MUTATED    52  12
  2P LOSS WILD-TYPE 596 216
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               64               812 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               12               216 
$`2P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-KL-8323 TCGA-KL-8324 
      102.81        28.11        47.24       130.13        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       24.79        73.91        54.74       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
      123.12       129.37        65.19       104.52        52.27        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       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 
      100.47       103.40        92.71        16.67       104.55       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3313 TCGA-A3-3374 TCGA-AK-3433 
       96.62        90.48        92.55        24.16        43.20       112.08 
TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4821 
       94.19        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 
       52.87        32.61        21.21        43.00        30.64        12.82 
TCGA-5P-A9K3 TCGA-5P-A9KH TCGA-BQ-5875 TCGA-HE-7130 
       15.48        67.43        86.76        58.19 

$`2P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
        3.58        80.68        74.17        54.77        12.33        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      103.43        46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
        6.74       109.22        98.33        71.41        28.80        62.37 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33        23.47        87.91        25.48        25.91 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 
        3.55         0.99        11.21       100.87        10.68       103.10 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       99.88        12.66        11.90        36.82         0.53        39.16 
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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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-3430 
       10.62        29.10       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       73.68        68.61       109.51        46.78        48.36        78.64 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-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-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
       28.47        19.00         1.38        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        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       74.20        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        4.01        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       16.90        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             2.50              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           153.73            194.79 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
           65.865            33.290 
[1] "2.5 - 153.7 (65.9)" "0.1 - 194.8 (33.3)"
[1] "hr=" "2.3"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2P LOSS MUTATED        20       24        14        5
  2P LOSS WILD-TYPE     434       79       176       99
D44V3, multiclass
           clus
vv          2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                20               434
  STAGE II               24                79
  STAGE III              14               176
  STAGE IV                5                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
  2P LOSS MUTATED    21  25  18   1
  2P LOSS WILD-TYPE 459 102 240  14
D44V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1              21               459
  T2              25               102
  T3              18               240
  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   3   2
  2P LOSS WILD-TYPE 288  41   4
D44V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0              35               288
  N1               3                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 504  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     42    2
  2P LOSS WILD-TYPE  504   87
   clus
vv  2P LOSS MUTATED 2P LOSS WILD-TYPE
  0              42               504
  1               2                87
[1] 2 2
[1] FALSE
D44V7, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    27  38
  2P LOSS WILD-TYPE 265 552
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     27   38
  2P LOSS WILD-TYPE  265  552
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              27               265
  MALE                38               552
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED    54   0
  2P LOSS WILD-TYPE 354   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     54    0
  2P LOSS WILD-TYPE  354    3
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO               54               354
  YES               0                 3
[1] 2 2
[1] FALSE
D44V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2P LOSS MUTATED                   46                                14
  2P LOSS WILD-TYPE                 20                               514
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2P LOSS MUTATED                                       5
  2P LOSS WILD-TYPE                                   283
D44V10, multiclass
                                       clus
vv                                      2P LOSS MUTATED 2P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 46                20
  KIDNEY CLEAR CELL RENAL CARCINOMA                  14               514
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               5               283
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
D44V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2P LOSS MUTATED                                  0     3
  2P LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED                           6    53
  2P LOSS WILD-TYPE                       115   666
D44V13, multiclass
                                  clus
vv                                 2P LOSS MUTATED 2P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                      6               115
  WHITE                                         53               666
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V14, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     3  33
  2P LOSS WILD-TYPE  39 589
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      3   33
  2P LOSS WILD-TYPE   39  589
                        clus
vv                       2P LOSS MUTATED 2P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              33               589
[1] 2 2
[1] FALSE

Clustering(45) Variable = 2Q LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  2Q LOSS MUTATED    51  11
  2Q LOSS WILD-TYPE 597 217
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               62               814 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               11               217 
$`2Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-KL-8323 TCGA-KL-8324 
      102.81        28.11        47.24       130.13        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       24.79        73.91        54.74       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 
      123.12       129.37        65.19       104.52        52.27        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       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 
      100.47       103.40        92.71        16.67       104.55       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 
       96.62        90.48        92.55        43.20       112.08        94.19 
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 
       52.87        32.61        21.21        43.00        30.64        12.82 
TCGA-5P-A9KH TCGA-HE-7130 
       67.43        58.19 

$`2Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 
        1.18         8.42        15.42       111.02        94.72        32.61 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 
        3.58        80.68        74.17        54.77        12.33        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       44.15        60.59        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      103.43        46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
        6.74       109.22        98.33        71.41        28.80        62.37 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       51.06        31.33        23.47        87.91        25.48        25.91 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 TCGA-KO-8410 
        3.55         0.99        11.21       100.87        10.68       103.10 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       99.88        12.66        11.90        36.82         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 
       15.78        73.68        68.61       109.51        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       78.64        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       72.89         1.41         3.32         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        19.00         1.38        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        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
       46.59         0.59         5.52        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4834 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        66.05        38.63        52.73        41.88        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       46.45        16.47        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       74.20        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             2.50              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           153.73            194.79 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           65.865            33.290 
[1] "2.5 - 153.7 (65.9)" "0.1 - 194.8 (33.3)"
[1] "hr=" "2.4"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  2Q LOSS MUTATED        19       24        14        5
  2Q LOSS WILD-TYPE     435       79       176       99
D45V3, multiclass
           clus
vv          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                19               435
  STAGE II               24                79
  STAGE III              14               176
  STAGE IV                5                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
  2Q LOSS MUTATED    20  24  18   1
  2Q LOSS WILD-TYPE 460 103 240  14
D45V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1              20               460
  T2              24               103
  T3              18               240
  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   3   2
  2Q LOSS WILD-TYPE 288  41   4
D45V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0              35               288
  N1               3                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 505  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     41    2
  2Q LOSS WILD-TYPE  505   87
   clus
vv  2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  0              41               505
  1               2                87
[1] 2 2
[1] FALSE
D45V7, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    26  37
  2Q LOSS WILD-TYPE 266 553
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     26   37
  2Q LOSS WILD-TYPE  266  553
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              26               266
  MALE                37               553
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED    53   0
  2Q LOSS WILD-TYPE 355   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     53    0
  2Q LOSS WILD-TYPE  355    3
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO               53               355
  YES               0                 3
[1] 2 2
[1] FALSE
D45V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  2Q LOSS MUTATED                   46                                14
  2Q LOSS WILD-TYPE                 20                               514
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  2Q LOSS MUTATED                                       3
  2Q LOSS WILD-TYPE                                   285
D45V10, multiclass
                                       clus
vv                                      2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 46                20
  KIDNEY CLEAR CELL RENAL CARCINOMA                  14               514
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               3               285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
D45V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  2Q LOSS MUTATED                                  0     3
  2Q LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED                           5    52
  2Q LOSS WILD-TYPE                       116   667
D45V13, multiclass
                                  clus
vv                                 2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                      5               116
  WHITE                                         52               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"
D45V14, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     3  33
  2Q LOSS WILD-TYPE  39 589
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3   33
  2Q LOSS WILD-TYPE   39  589
                        clus
vv                       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              33               589
[1] 2 2
[1] FALSE

Clustering(46) Variable = 3P LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED   276 134
  3P LOSS WILD-TYPE 372  94
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              410               466 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
              134                94 
$`3P LOSS MUTATED`
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        38.47        34.29        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        19.73        52.21        18.51 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B8-5162 TCGA-B8-A54H 
      133.94        15.78        70.68       119.38         1.18         8.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 
       54.77        12.33        11.64         6.94        61.51        25.81 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       62.86        49.15        27.02        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       75.58         0.59         5.46        43.69        45.96        12.16 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-A4-A5Y1 
       37.15        66.28        56.84        81.21        23.01        12.99 
TCGA-B9-A44B TCGA-BQ-5892 TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8333 TCGA-KN-8421 
       11.87        11.97         6.74       153.73        98.33        87.91 
TCGA-KN-8425 TCGA-KN-8432 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-3Z-A93Z 
      104.52         2.50       104.55       105.60        96.62        12.66 
TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       36.82        39.16        24.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3331 TCGA-A3-3335 
       49.58        48.59        36.36        38.99        48.82        62.01 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3365 
        4.50        52.93        29.92        18.44        88.37        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-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        18.87        28.31        20.28        33.47        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-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
       78.64        94.29        38.40        82.45        72.89         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-B0-4710 TCGA-B0-4713 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4816 
       57.70         6.64        15.72        46.59         0.59        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-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 
       27.42         6.71        56.68        10.52        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       43.30        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5110 
       52.08        15.95        90.87        90.48        58.59        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 
       38.63        52.73        41.88        51.02        38.43        46.39 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        71.41        73.84       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-5633 
      131.15        89.49        91.46        35.90        31.96        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
       32.98        21.57        16.67        12.00         5.10         1.25 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       49.97        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F 
        0.85         6.38         0.53        34.39        14.30        17.06 
TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4159 TCGA-BP-4163 
        1.74         4.93        17.36        16.27        85.51        93.34 
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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4340 
       97.45        27.78        62.07        37.25        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4758 
       52.24        62.86        49.08        44.94        31.89        72.59 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 
        5.98        41.75        71.80        48.07        13.15         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4797 
       61.97        13.51        56.91        68.38        48.95        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95         6.71        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
       58.68        60.30        61.22        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 
       31.30        36.95         3.88        46.45        16.47        30.64 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5173 
       18.51        37.02        35.21        28.87         6.35         2.04 
TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       74.20        52.27        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       37.22        13.35        33.24        13.41        24.62        33.47 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4640 
       34.95         0.95       115.00        46.55        73.22       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       79.66        74.27        75.06        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4892 TCGA-CJ-4893 
       61.91        64.18        30.64        51.52        50.01        24.66 
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-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 
       49.18        49.28        50.33        45.14         3.06       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CJ-6033 
      122.83        62.10        73.35        53.42       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
       64.57        81.83         5.39        73.18        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       74.66       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
       69.21        58.75         6.77        63.39        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5982 TCGA-CZ-5984 
       69.96        84.30        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-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
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-MW-A4EC TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K9 
       19.96        16.37        54.64        51.52        38.99        19.36 
TCGA-A4-A57E TCGA-AL-3473 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5882 TCGA-DZ-6131 
        8.48        62.66        14.86         8.88        21.63        79.86 
TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        4.01        23.08         3.68         2.04        10.55        14.07 
TCGA-UZ-A9PQ TCGA-WN-A9G9 
       86.27        26.01 

$`3P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3343 TCGA-B0-4712 TCGA-B0-5691 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       31.07        43.96       112.80       126.05        24.82        25.91 
TCGA-B8-A54K TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 
       15.42        77.62        44.15        60.59        20.38        37.25 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-5191 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4862 
       53.65        27.22        31.79       103.43        46.16       107.54 
TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5576 TCGA-G6-A8L7 TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       65.88        11.67        23.90        70.13        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ 
       67.17        61.05        21.37         0.89        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       26.04        13.25        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
       15.91        15.62        38.07        23.84       109.22       137.06 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 
       90.48       108.62        98.96        84.89        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91        65.19         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 TCGA-6D-AA2E 
       16.67       103.10        99.88        90.48        92.55        11.90 
TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3374 
        0.53        37.38        45.53        51.25        10.49        43.20 
TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
       65.52       117.80       122.56        94.19        46.78        48.36 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 
       40.01        83.21        37.58        12.13        40.70         3.32 
TCGA-B0-4691 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        4.57        19.00         1.38         3.62        65.10         7.82 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4814 TCGA-B0-4834 TCGA-B0-4839 TCGA-B0-4844 
        3.25        58.45         5.52        68.71        53.88        10.29 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5100 TCGA-B0-5106 
       11.24        11.90         7.30        25.32        62.89        52.54 
TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5705 
       30.48        19.30        52.87        48.82        56.98       149.16 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4101 TCGA-B2-4102 TCGA-B4-5378 TCGA-B4-5835 
       32.61         1.68        21.30        31.30         5.75         0.53 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5165 TCGA-B8-5545 
       42.71        25.05        45.37        17.19        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A8YJ TCGA-BP-4161 
       16.60        48.53        27.29        29.88        14.17        90.28 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4334 
      101.06        99.85        62.24        54.90        53.42        21.21 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       15.62         0.07        12.23        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4784 TCGA-BP-4787 
       12.30        77.98        61.68        10.82        60.95        15.78 
TCGA-BP-4790 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       36.53        47.97         6.74        57.40        58.98        14.24 
TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 
       43.00        38.70        37.48        79.30        30.64         9.63 
TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5198 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4872 
       22.78        23.47        19.82        14.17       106.16        47.18 
TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 
      116.84        57.83       113.46        63.98       115.69       109.84 
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-CZ-4861 
       67.00        62.66        92.02        85.78         1.35        14.66 
TCGA-CZ-4866 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-DV-A4VZ TCGA-EU-5904 
      107.41         2.40        31.10        12.69        12.00        18.12 
TCGA-EU-5905 TCGA-G6-A5PC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
        3.91         7.96        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       66.71        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76        19.27        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        12.36        12.76        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
      110.73        51.35        31.73        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           153.73            194.79 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           39.745            30.330 
[1] "0.1 - 153.7 (39.7)" "0.1 - 194.8 (30.3)"
[1] "hr=" "1.5"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3P LOSS MUTATED       190       49       112       57
  3P LOSS WILD-TYPE     264       54        78       47
D46V3, multiclass
           clus
vv          3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I               190               264
  STAGE II               49                54
  STAGE III             112                78
  STAGE IV               57                47
[1] 4 2
[1] TRUE
[1] "dimension of 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   195  61 151   4
  3P LOSS WILD-TYPE 285  66 107  11
D46V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1             195               285
  T2              61                66
  T3             151               107
  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   179  17   2
  3P LOSS WILD-TYPE 144  27   4
D46V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0             179               144
  N1              17                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"
D46V6, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   316  53
  3P LOSS WILD-TYPE 230  36
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    316   53
  3P LOSS WILD-TYPE  230   36
   clus
vv  3P LOSS MUTATED 3P LOSS WILD-TYPE
  0             316               230
  1              53                36
[1] 2 2
[1] FALSE
D46V7, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   134 277
  3P LOSS WILD-TYPE 158 313
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    134  277
  3P LOSS WILD-TYPE  158  313
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE             134               158
  MALE               277               313
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED   121   2
  3P LOSS WILD-TYPE 287   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED    121    2
  3P LOSS WILD-TYPE  287    1
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO              121               287
  YES               2                 1
[1] 2 2
[1] FALSE
D46V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3P LOSS MUTATED                    8                               381
  3P LOSS WILD-TYPE                 58                               147
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3P LOSS MUTATED                                      22
  3P LOSS WILD-TYPE                                   266
D46V10, multiclass
                                       clus
vv                                      3P LOSS MUTATED 3P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  8                58
  KIDNEY CLEAR CELL RENAL CARCINOMA                 381               147
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              22               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"
D46V11, continuous
D46V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3P LOSS MUTATED                                  0     6
  3P LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED                          39   359
  3P LOSS WILD-TYPE                        82   360
D46V13, multiclass
                                  clus
vv                                 3P LOSS MUTATED 3P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          6                10
  BLACK OR AFRICAN AMERICAN                     39                82
  WHITE                                        359               360
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V14, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    21 272
  3P LOSS WILD-TYPE  21 350
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     21  272
  3P LOSS WILD-TYPE   21  350
                        clus
vv                       3P LOSS MUTATED 3P LOSS WILD-TYPE
  HISPANIC OR LATINO                  21                21
  NOT HISPANIC OR LATINO             272               350
[1] 2 2
[1] FALSE

Clustering(47) Variable = 3Q LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED    81  38
  3Q LOSS WILD-TYPE 567 190
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
              119               757 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               38               190 
$`3Q LOSS MUTATED`
TCGA-AK-3425 TCGA-B0-4815 TCGA-BP-4158 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
      109.91        52.21       111.02        74.17        54.77        12.33 
TCGA-BP-4986 TCGA-BP-4999 TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4904 
       25.81        41.62        27.02        44.55       105.37       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-DV-5573 TCGA-DV-5574 TCGA-KL-8324 TCGA-KN-8421 
       53.26       118.85        37.15        66.28       153.73        87.91 
TCGA-KN-8425 TCGA-KN-8432 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-A3-3313 
      104.52         2.50       104.55       105.60        96.62        24.16 
TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 
       49.02        48.59        38.99         4.50        52.93        88.37 
TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI 
       28.70        24.16        18.64        18.87        20.28        33.47 
TCGA-A3-A6NN TCGA-AK-3433 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4696 
        0.10       112.08        82.45         1.41         2.53        28.47 
TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4836 TCGA-B0-4845 
       46.59        33.50        36.53        14.93        40.70        65.29 
TCGA-B0-5094 TCGA-B0-5099 TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5703 TCGA-B0-5712 
       10.95        15.95        52.73        38.43        73.84        89.49 
TCGA-B2-3924 TCGA-B2-5639 TCGA-B8-4148 TCGA-B8-5163 TCGA-B8-A54I TCGA-BP-4163 
       35.90        32.98        49.97        27.02         4.93        93.34 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4329 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4763 
        0.43        23.05        27.78        44.94        31.89        41.75 
TCGA-BP-4768 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
       13.15        56.91        68.38        36.39        36.95         6.71 
TCGA-BP-4963 TCGA-BP-4977 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5173 
       60.30        14.93        16.47        30.64        35.21         2.04 
TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5195 TCGA-BP-5200 TCGA-CJ-4635 
       74.40        37.22        13.35        24.62        34.95        46.55 
TCGA-CJ-4644 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4907 
       11.05        74.27        75.06        66.21        51.52        49.28 
TCGA-CJ-5679 TCGA-CJ-5682 TCGA-CW-5580 TCGA-CW-6090 TCGA-CZ-4863 TCGA-CZ-4864 
       22.32       122.83        64.57        83.90        63.39        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 
       63.42        58.82        23.74        79.63        90.54        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5986 
       10.85        10.22        21.76         1.94        67.96        12.26 
TCGA-CZ-5987 TCGA-EU-5907 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-2Z-A9JG TCGA-5P-A9K9 
       14.63         4.18         2.01        19.96        54.64        19.36 
TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7966 
        8.88        21.63         4.01        23.08         3.68 

$`3Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-5088 
       58.49        28.73        22.45        19.73        43.96        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4160 
       24.82        25.91         1.18         8.42        15.42        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       32.61         3.58        80.68        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
       27.22         5.82        45.07        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 
       62.86        49.15        31.79        31.27        63.25        26.93 
TCGA-CJ-4894 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
       27.65        75.58       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        43.69        45.96        65.88        12.16        11.67 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
        6.74        38.07        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.48        25.91        65.19         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12        19.33        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       16.67       103.10        99.88        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3319 
       11.90        36.82         0.53        39.16        49.08        37.15 
TCGA-A3-3320 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3349 
       49.58        36.36        37.38        48.82        62.01        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 
       29.92        18.44        51.25        10.49        74.63        74.76 
TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 TCGA-A3-3385 
       53.29        43.20        55.76        20.71        28.31        65.52 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       15.39        22.65         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 
       94.29        83.21        37.58        38.40        72.89        12.13 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4697 
       40.70         3.32         1.41         4.57         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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
       57.70         6.64         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4824 
        5.52        45.07        16.77         6.02        40.44        54.48 
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-B0-4846 
       53.88         6.71        56.68        10.52        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-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
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        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
       38.63        41.88        52.87        51.02        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        71.41       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
       79.89       131.15        91.46        32.61         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       21.30        31.30        31.66        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 
        0.36         0.23        23.31        16.80        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        1.74        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
      101.06        99.85        89.36        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 
       64.27        54.90        97.45        53.42        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       62.86        49.08        12.23        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
       12.30        72.59        77.98         5.98        71.80        48.07 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4784 
       61.68        10.82         5.33        61.97        13.51        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4804 TCGA-BP-4959 
       15.78        48.95        36.53        10.98        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       71.41        63.62        58.68        61.22         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         6.94 
TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 
       47.11        36.07        33.34        46.45        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        3.88        46.45        43.00        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       37.48        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       52.27         9.63        38.30        42.44        37.25        22.78 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 
       33.24        23.47        13.41        33.47        19.82         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
      116.84        64.27        71.87        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       64.18        30.64        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       51.29        49.18        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 
      133.71        25.71        18.87        25.25        18.15        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-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-6097 TCGA-CZ-4853 
       78.18        74.66         1.35       105.93        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4866 
       47.08        69.21        58.75         6.77        14.66       107.41 
TCGA-CZ-5453 TCGA-CZ-5455 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5465 
       79.53        18.44        91.69        94.45        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       22.52         2.40        31.10        12.69        80.19        65.65 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-MW-A4EC 
        6.77         7.96        10.29        35.87        19.43        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       78.64        15.48        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
       19.27        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        0.43        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       25.15        20.52        25.84        25.25        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-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           153.73            194.79 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            37.15             34.49 
[1] "0.1 - 153.7 (37.1)" "0.1 - 194.8 (34.5)"
[1] "hr=" "1.2"
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  3Q LOSS MUTATED        54       20        26       18
  3Q LOSS WILD-TYPE     400       83       164       86
D47V3, multiclass
           clus
vv          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                54               400
  STAGE II               20                83
  STAGE III              26               164
  STAGE IV               18                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
  3Q LOSS MUTATED    57  23  39   0
  3Q LOSS WILD-TYPE 423 104 219  15
D47V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1              57               423
  T2              23               104
  T3              39               219
  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
  3Q LOSS MUTATED    49   3   2
  3Q LOSS WILD-TYPE 274  41   4
D47V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0              49               274
  N1               3                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"
D47V6, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    89  17
  3Q LOSS WILD-TYPE 457  72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     89   17
  3Q LOSS WILD-TYPE  457   72
   clus
vv  3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  0              89               457
  1              17                72
[1] 2 2
[1] FALSE
D47V7, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    29  90
  3Q LOSS WILD-TYPE 263 500
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     29   90
  3Q LOSS WILD-TYPE  263  500
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              29               263
  MALE                90               500
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED    29   2
  3Q LOSS WILD-TYPE 379   1
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     29    2
  3Q LOSS WILD-TYPE  379    1
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO               29               379
  YES               2                 1
[1] 2 2
[1] FALSE
D47V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  3Q LOSS MUTATED                    7                               105
  3Q LOSS WILD-TYPE                 59                               423
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  3Q LOSS MUTATED                                       7
  3Q LOSS WILD-TYPE                                   281
D47V10, multiclass
                                       clus
vv                                      3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  7                59
  KIDNEY CLEAR CELL RENAL CARCINOMA                 105               423
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2               104 
       TCGA-B8-4621        TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-2Z-A9JD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JQ        TCGA-5P-A9JU        TCGA-B9-A44B        TCGA-DW-5561 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-7834        TCGA-DW-7838        TCGA-GL-A59T        TCGA-IZ-A6M8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR        TCGA-Y8-A8RZ 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       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-AK-3445        TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-4146 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B8-5158        TCGA-B8-5164        TCGA-B8-5550        TCGA-B8-A54E 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B8-A54F        TCGA-B8-A54G        TCGA-B8-A8YJ        TCGA-DV-A4VX 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G6-A5PC        TCGA-MM-A563        TCGA-T7-A92I        TCGA-2Z-A9J2 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9J5        TCGA-2Z-A9J7        TCGA-2Z-A9J8        TCGA-2Z-A9JI 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JK        TCGA-2Z-A9JM        TCGA-2Z-A9JN        TCGA-2Z-A9JO 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-4A-A93W        TCGA-4A-A93Y        TCGA-5P-A9K3        TCGA-5P-A9KE 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A4-8310        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3466        TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4114        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-A69E        TCGA-DW-7963        TCGA-F9-A97G        TCGA-G7-6792 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        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-A9DD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-HE-A5NJ        TCGA-HE-A5NK        TCGA-IA-A40U 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-IA-A83S        TCGA-IA-A83V        TCGA-MH-A854        TCGA-MH-A856 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-P4-A5E7        TCGA-P4-A5EB        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        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" 
D47V12, continuous
[1] "Remove cluster labels:" "3Q LOSS MUTATED"       
clus
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                1                73 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-2Z-A9JD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445        TCGA-AK-3451 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550        TCGA-MM-A563 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-T7-A92I        TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        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-A9DD 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" "3Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        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 
"3Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  3Q LOSS MUTATED                                  0     1
  3Q LOSS WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED                           8   107
  3Q LOSS WILD-TYPE                       113   612
D47V13, multiclass
                                  clus
vv                                 3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      8               113
  WHITE                                        107               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"
D47V14, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     6  70
  3Q LOSS WILD-TYPE  36 552
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      6   70
  3Q LOSS WILD-TYPE   36  552
                        clus
vv                       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              70               552
[1] 2 2
[1] FALSE

Clustering(48) Variable = 4P LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                 0   1
  4P LOSS MUTATED    47  51
  4P LOSS WILD-TYPE 601 177
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               98               778 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               51               177 
$`4P LOSS MUTATED`
TCGA-B0-4707 TCGA-B0-4712 TCGA-B8-5162 TCGA-BP-4164 TCGA-BP-4353 TCGA-BP-4762 
       19.73        43.96         1.18        32.61        12.33        44.15 
TCGA-CJ-4894 TCGA-CJ-6030 TCGA-G6-A8L7 TCGA-AL-A5DJ TCGA-KN-8427 TCGA-A3-3316 
       27.65        75.58        70.13        49.25         0.99        49.08 
TCGA-A3-3352 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3385 TCGA-AK-3436 TCGA-AK-3458 
       18.44        53.29        18.64        65.52       109.51        38.40 
TCGA-B0-4690 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 
        1.41        57.70        46.59         5.52        40.44        36.53 
TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 
       10.09        10.29        65.29        36.85         7.30         8.05 
TCGA-B0-5098 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5399 TCGA-B4-5835 TCGA-B4-5838 
       52.08        38.63        41.88        46.39         0.53         5.46 
TCGA-B8-4143 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4343 
       23.31        45.37        40.04         6.38        90.28        62.86 
TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4974 TCGA-BP-5173 
       31.89        13.15        10.82        15.78         6.94         2.04 
TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4644 TCGA-CJ-4878 TCGA-CJ-4897 
       42.44        33.47        19.82        11.05        71.87       109.84 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4913 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 
       51.29        49.28        38.56       133.71        25.71        22.32 
TCGA-CJ-6028 TCGA-CW-5580 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 
       53.42        64.57        66.31        83.90        18.77        47.08 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 
       69.21         6.77       107.41        90.54        10.85        84.30 
TCGA-CZ-5469 TCGA-EU-5907 TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 
       31.10         4.18        51.52        12.82        15.48        19.36 
TCGA-A4-7287 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5894 
       19.63        37.51        29.03        22.92        21.63         2.76 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 
       79.86        10.68        13.08        20.52        16.90         3.68 
TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA 
       58.19        73.25         2.04        10.55        42.94         6.61 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       14.07        18.02 

$`4P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 
      109.91        58.49        28.73        22.45        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       24.82        25.91         8.42        15.42       111.02        94.72 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4775 
        3.58        80.68        74.17        54.77        77.62        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4904 
       44.55        31.27        63.25       105.37        26.93       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85       103.43        46.16         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-MM-A84U 
       37.15        66.28        56.84        23.90        81.21        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        76.64        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       21.86        11.87        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
       90.48       108.62        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-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-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       99.88       105.60        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 
       11.90        36.82         0.53        39.16        24.16        49.02 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       37.15        49.58        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       48.82        62.01         4.50        52.93        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
       24.16        43.20        55.76        20.71        18.87        28.31 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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-B0-4713 
        3.62        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 
        3.25        58.45        15.72         0.59        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-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       56.68        10.52        39.45        26.07        29.03         2.27 
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-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       15.09        10.95         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
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        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 
       42.71        25.05        17.19        25.55        50.14        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        50.14        16.60        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
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-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 
        0.07        93.99        18.48        52.24        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        74.40        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-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16       114.41        54.61        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 
       39.45        50.24        56.35        47.67        49.97        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        54.48        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
      131.08        72.00       129.40        18.87        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
      122.83        62.10        73.35        67.00        62.66       119.64 
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-CZ-4853 TCGA-CZ-4859 
       78.18        74.66         1.35       105.93        25.45        58.75 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        69.96        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 
        6.77         7.96        10.29        35.87         2.01        19.43 
TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       54.64        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA 
       22.26        78.64        71.80        62.93        43.04        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        67.43        18.21         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         0.95         7.92       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        7.17         3.81        40.77        80.88        51.19        74.60 
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        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        25.84        25.25        17.98        23.08        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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.53              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           133.71            194.79 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           31.495            36.215 
[1] "0.5 - 133.7 (31.5)" "0.1 - 194.8 (36.2)"
[1] "hr=" "2.8"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4P LOSS MUTATED        25        7        40       23
  4P LOSS WILD-TYPE     429       96       150       81
D48V3, multiclass
           clus
vv          4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                25               429
  STAGE II                7                96
  STAGE III              40               150
  STAGE IV               23                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
  4P LOSS MUTATED    27  11  55   5
  4P LOSS WILD-TYPE 453 116 203  10
D48V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1              27               453
  T2              11               116
  T3              55               203
  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  14   1
  4P LOSS WILD-TYPE 287  30   5
D48V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              36               287
  N1              14                30
  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"
D48V6, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    61  19
  4P LOSS WILD-TYPE 485  70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     61   19
  4P LOSS WILD-TYPE  485   70
   clus
vv  4P LOSS MUTATED 4P LOSS WILD-TYPE
  0              61               485
  1              19                70
[1] 2 2
[1] FALSE
D48V7, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    41  57
  4P LOSS WILD-TYPE 251 533
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     41   57
  4P LOSS WILD-TYPE  251  533
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              41               251
  MALE                57               533
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                  0   1
  4P LOSS MUTATED    35   0
  4P LOSS WILD-TYPE 373   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     35    0
  4P LOSS WILD-TYPE  373    3
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO               35               373
  YES               0                 3
[1] 2 2
[1] FALSE
D48V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4P LOSS MUTATED                    1                                72
  4P LOSS WILD-TYPE                 65                               456
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4P LOSS MUTATED                                      25
  4P LOSS WILD-TYPE                                   263
D48V10, multiclass
                                       clus
vv                                      4P LOSS MUTATED 4P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  72               456
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              25               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"
D48V11, continuous
D48V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4P LOSS MUTATED                                  0     3
  4P LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED                           7    82
  4P LOSS WILD-TYPE                       114   637
D48V13, multiclass
                                  clus
vv                                 4P LOSS MUTATED 4P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                      7               114
  WHITE                                         82               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"
D48V14, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     6  67
  4P LOSS WILD-TYPE  36 555
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      6   67
  4P LOSS WILD-TYPE   36  555
                        clus
vv                       4P LOSS MUTATED 4P LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              67               555
[1] 2 2
[1] FALSE

Clustering(49) Variable = 4Q LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                 0   1
  4Q LOSS MUTATED    43  49
  4Q LOSS WILD-TYPE 605 179
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               92               784 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               49               179 
$`4Q LOSS MUTATED`
TCGA-B0-4707 TCGA-B0-4712 TCGA-B8-5162 TCGA-BP-4164 TCGA-BP-4353 TCGA-AL-A5DJ 
       19.73        43.96         1.18        32.61        12.33        49.25 
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-B0-4710 TCGA-B0-4811 
      109.51        38.40         3.32         1.41        57.70        46.59 
TCGA-B0-4814 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-4845 
        5.52        40.44        36.53        10.09        10.29        65.29 
TCGA-B0-4852 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5098 TCGA-B0-5113 TCGA-B0-5116 
       36.85         7.30         8.05        52.08        38.63        41.88 
TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-5158 TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4343 
        5.46        23.31        40.04         6.38        90.28        62.86 
TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4974 TCGA-BP-5173 
       31.89        13.15        10.82        15.78         6.94         2.04 
TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4644 TCGA-CJ-4881 TCGA-CJ-4897 
       42.44        33.47        19.82        11.05        66.21       109.84 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 
       51.29        49.28       133.71        25.71        22.32        53.42 
TCGA-CW-5580 TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 
       64.57        66.31        83.90        18.77        47.08        69.21 
TCGA-CZ-4860 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 
        6.77       107.41        90.54        10.85        84.30        31.10 
TCGA-EU-5907 TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7287 
        4.18        51.52        12.82        15.48        19.36        19.63 
TCGA-A4-A57E TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-BQ-5894 
        8.48        37.51        29.03        19.27        21.63         2.76 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7966 
       79.86        10.68        13.08        20.52        16.90         3.68 
TCGA-HE-7130 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5E8 TCGA-P4-A5EA 
       58.19        73.25         2.04        10.55        42.94         6.61 
TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       14.07        18.02 

$`4Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 
      109.91        58.49        28.73        22.45        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       24.82        25.91         8.42        15.42       111.02        94.72 
TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
        3.58        80.68        74.17        54.77        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       31.79        44.55        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
       96.62        90.48        92.55        12.66        11.90        36.82 
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-A3-3322 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        62.01 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        29.92        88.37        51.25        10.49 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 
       28.70        74.63        74.76        24.16        43.20        55.76 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.87        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
      112.08        68.61        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       40.01        94.29        83.21        37.58        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       12.13        40.70         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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        5.98         2.14         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 
        0.59        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        10.52        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-B0-5092 TCGA-B0-5094 TCGA-B0-5096 
       11.24        11.90        25.32        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        58.59        19.30        66.05        52.73        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         1.25         0.53 
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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 
       25.05        45.37        17.19        25.55        50.14        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        50.14        16.60        48.53 
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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
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-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 
        0.07        93.99        18.48        52.24        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38        45.50        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87         6.35        79.30        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 
       52.27         9.63        74.40        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-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16       114.41        54.61        58.95        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       64.27        71.87        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 
       39.45        50.24        56.35        47.67        49.97        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-5678 TCGA-CJ-5680 
       18.81       131.08        72.00       129.40        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 
       18.15       122.83        62.10        73.35        67.00        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 
      119.64         7.36        92.02        81.83         5.39        85.78 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CZ-4853 
       73.18        78.18        74.66         1.35       105.93        25.45 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
       58.75        14.66        63.39        93.04        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
       79.53        23.74        18.44        79.63        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       94.45        10.22        21.76        69.96        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
        1.94        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        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-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        54.64        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       90.21        22.26        78.64        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
       10.82         7.66         0.95         7.92       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        7.17         3.81        40.77        80.88        51.19        74.60 
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        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        25.84        25.25        17.98        23.08        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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.99              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           133.71            194.79 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           22.815            36.675 
[1] "1.0 - 133.7 (22.8)" "0.1 - 194.8 (36.7)"
[1] "hr=" "3"  
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  4Q LOSS MUTATED        20        7        37       25
  4Q LOSS WILD-TYPE     434       96       153       79
D49V3, multiclass
           clus
vv          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                20               434
  STAGE II                7                96
  STAGE III              37               153
  STAGE IV               25                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
  4Q LOSS MUTATED    22  12  52   6
  4Q LOSS WILD-TYPE 458 115 206   9
D49V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1              22               458
  T2              12               115
  T3              52               206
  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  13   1
  4Q LOSS WILD-TYPE 292  31   5
D49V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              31               292
  N1              13                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"
D49V6, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    54  21
  4Q LOSS WILD-TYPE 492  68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     54   21
  4Q LOSS WILD-TYPE  492   68
   clus
vv  4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  0              54               492
  1              21                68
[1] 2 2
[1] FALSE
D49V7, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    34  58
  4Q LOSS WILD-TYPE 258 532
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     34   58
  4Q LOSS WILD-TYPE  258  532
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              34               258
  MALE                58               532
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED    32   0
  4Q LOSS WILD-TYPE 376   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     32    0
  4Q LOSS WILD-TYPE  376    3
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO               32               376
  YES               0                 3
[1] 2 2
[1] FALSE
D49V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  4Q LOSS MUTATED                    1                                65
  4Q LOSS WILD-TYPE                 65                               463
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  4Q LOSS MUTATED                                      26
  4Q LOSS WILD-TYPE                                   262
D49V10, multiclass
                                       clus
vv                                      4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                  65               463
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              26               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"
D49V11, continuous
D49V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  4Q LOSS MUTATED                                  0     3
  4Q LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED                           6    77
  4Q LOSS WILD-TYPE                       115   642
D49V13, multiclass
                                  clus
vv                                 4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                      6               115
  WHITE                                         77               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"
D49V14, binary
                   cls
clus                  0   1
  4Q LOSS MUTATED     5  62
  4Q LOSS WILD-TYPE  37 560
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   62
  4Q LOSS WILD-TYPE   37  560
                        clus
vv                       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   5                37
  NOT HISPANIC OR LATINO              62               560
[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 636 217
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               23               853 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               11               217 
$`5P LOSS MUTATED`
TCGA-KM-8442 TCGA-CZ-4854 TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 
       47.24        46.16       153.73       108.62        24.79        62.37 
TCGA-KM-8438 TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 TCGA-AK-3433 TCGA-B0-4688 
      151.96        19.33       100.47       104.55       112.08         3.32 
TCGA-B0-5107 TCGA-B8-4143 TCGA-BP-4770 TCGA-CJ-4901 TCGA-CZ-5469 TCGA-A4-7286 
       30.48        23.31        10.82        47.67        31.10        18.21 
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-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-A3-3307 
      102.81        28.11        23.28        28.80       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 
       92.55        30.25        44.84        86.56        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       71.41        28.80        54.74        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47        10.68       103.40        92.71        16.67 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.87        90.48        52.54        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      129.67        85.78        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         1.25         0.53         4.64 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        5.46         0.36         0.23        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        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        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        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-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-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-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       19.00        24.89        13.08         2.40         1.18         0.43 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.78        90.90        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
       42.94        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.76              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           153.73            194.79 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            30.48             35.93 
[1] "2.8 - 153.7 (30.5)" "0.1 - 194.8 (35.9)"
[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     452       94       185       97
D50V3, multiclass
           clus
vv          5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                 2               452
  STAGE II                9                94
  STAGE III               5               185
  STAGE IV                7                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
  5P LOSS MUTATED     2  10  10   2
  5P LOSS WILD-TYPE 478 117 248  13
D50V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               2               478
  T2              10               117
  T3              10               248
  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    13   3   2
  5P LOSS WILD-TYPE 310  41   4
D50V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              13               310
  N1               3                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"
D50V6, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    12   4
  5P LOSS WILD-TYPE 534  85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12    4
  5P LOSS WILD-TYPE  534   85
   clus
vv  5P LOSS MUTATED 5P LOSS WILD-TYPE
  0              12               534
  1               4                85
[1] 2 2
[1] FALSE
D50V7, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    12  12
  5P LOSS WILD-TYPE 280 578
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     12   12
  5P LOSS WILD-TYPE  280  578
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              12               280
  MALE                12               578
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    14   0
  5P LOSS WILD-TYPE 394   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     14    0
  5P LOSS WILD-TYPE  394    3
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO               14               394
  YES               0                 3
[1] 2 2
[1] FALSE
D50V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5P LOSS MUTATED                   10                                 8
  5P LOSS WILD-TYPE                 56                               520
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5P LOSS MUTATED                                       6
  5P LOSS WILD-TYPE                                   282
D50V10, multiclass
                                       clus
vv                                      5P LOSS MUTATED 5P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                   8               520
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               6               282
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
D50V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5P LOSS MUTATED                                  0     1
  5P LOSS WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED                           2    18
  5P LOSS WILD-TYPE                       119   701
D50V13, multiclass
                                  clus
vv                                 5P LOSS MUTATED 5P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      2               119
  WHITE                                         18               701
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V14, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     3  14
  5P LOSS WILD-TYPE  39 608
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      3   14
  5P LOSS WILD-TYPE   39  608
                        clus
vv                       5P LOSS MUTATED 5P LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              14               608
[1] 2 2
[1] FALSE

Clustering(51) Variable = 5Q LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                 0   1
  5Q LOSS MUTATED    13   9
  5Q LOSS WILD-TYPE 635 219
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               22               854 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                9               219 
$`5Q LOSS MUTATED`
TCGA-KM-8442 TCGA-CZ-4854 TCGA-KL-8324 TCGA-KL-8330 TCGA-KL-8341 TCGA-KL-8346 
       47.24        46.16       153.73       108.62        24.79        62.37 
TCGA-KM-8438 TCGA-KN-8431 TCGA-KO-8405 TCGA-KO-8409 TCGA-AK-3433 TCGA-B0-4688 
      151.96        19.33       100.47       104.55       112.08         3.32 
TCGA-BP-4770 TCGA-CJ-4901 TCGA-CZ-5469 TCGA-A4-7286 TCGA-A4-7287 TCGA-BQ-5879 
       10.82        47.67        31.10        18.21        19.63        22.92 
TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-GL-7966 TCGA-P4-A5EA 
        2.76        10.68         3.68         6.61 

$`5Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-A3-3307 
      102.81        28.11        23.28        28.80       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        5.46        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-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8326 
       15.91        15.62         6.74        38.07        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48        98.96        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 
       92.55        30.25        44.84        86.56        66.54        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       71.41        28.80        54.74        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       87.12         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47        10.68       103.40        92.71        16.67 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68        68.61       109.51        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
       38.40        82.45        72.89        12.13        40.70         1.41 
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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       13.15        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       50.24        56.35        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       18.77        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        63.39        93.04       107.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
       79.53        23.74        18.44        79.63        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       16.37        11.70         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG 
      100.27        56.91         4.57        91.73        56.81        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       51.52        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       43.04        19.36        12.99        12.39        27.09        67.43 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        7.66         0.95         7.92       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       23.08        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             2.76              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           153.73            194.79 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           27.945            35.915 
[1] "2.8 - 153.7 (27.9)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1.5"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  5Q LOSS MUTATED         3        9         6        4
  5Q LOSS WILD-TYPE     451       94       184      100
D51V3, multiclass
           clus
vv          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                 3               451
  STAGE II                9                94
  STAGE III               6               184
  STAGE IV                4               100
[1] 4 2
[1] TRUE
[1] "dimension of 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     3   9   9   2
  5Q LOSS WILD-TYPE 477 118 249  13
D51V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               3               477
  T2               9               118
  T3               9               249
  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    11   4   1
  5Q LOSS WILD-TYPE 312  40   5
D51V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              11               312
  N1               4                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"
D51V6, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    12   2
  5Q LOSS WILD-TYPE 534  87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     12    2
  5Q LOSS WILD-TYPE  534   87
   clus
vv  5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  0              12               534
  1               2                87
[1] 2 2
[1] FALSE
D51V7, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    11  12
  5Q LOSS WILD-TYPE 281 578
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     11   12
  5Q LOSS WILD-TYPE  281  578
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              11               281
  MALE                12               578
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    15   0
  5Q LOSS WILD-TYPE 393   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     15    0
  5Q LOSS WILD-TYPE  393    3
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO               15               393
  YES               0                 3
[1] 2 2
[1] FALSE
D51V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  5Q LOSS MUTATED                   10                                 6
  5Q LOSS WILD-TYPE                 56                               522
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  5Q LOSS MUTATED                                       7
  5Q LOSS WILD-TYPE                                   281
D51V10, multiclass
                                       clus
vv                                      5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                   6               522
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               7               281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
D51V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  5Q LOSS MUTATED                                  0     1
  5Q LOSS WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED                           2    17
  5Q LOSS WILD-TYPE                       119   702
D51V13, multiclass
                                  clus
vv                                 5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      2               119
  WHITE                                         17               702
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V14, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     3  13
  5Q LOSS WILD-TYPE  39 609
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      3   13
  5Q LOSS WILD-TYPE   39  609
                        clus
vv                       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   3                39
  NOT HISPANIC OR LATINO              13               609
[1] 2 2
[1] FALSE

Clustering(52) Variable = 6P LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                 0   1
  6P LOSS MUTATED   122  48
  6P LOSS WILD-TYPE 526 180
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
              170               706 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               48               180 
$`6P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3336 TCGA-B0-4707 
      102.81        28.11        47.24       130.13        34.29        19.73 
TCGA-B0-4712 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4775 
       43.96        32.61         3.58        74.17        12.33        60.59 
TCGA-BP-4986 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4904 TCGA-CJ-6027 
       25.81        62.86        31.79        31.27       108.56       118.85 
TCGA-DV-5568 TCGA-G6-A8L7 TCGA-5P-A9JU TCGA-BQ-7056 TCGA-KL-8323 TCGA-KL-8324 
       12.16        70.13        12.26        20.12        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
       23.84       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 
       66.54        24.79        73.91        54.74       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       49.97       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 
      104.52        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       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       104.55       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3335 TCGA-A3-3346 
       92.55        36.82        49.08        37.15        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 TCGA-AK-3426 
       52.93        18.44        43.20        18.64        18.87        29.10 
TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 
       15.78       112.08        68.61       109.51        94.19        40.01 
TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 
       38.40        12.13        40.70         1.41         3.48        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 
        1.38         3.62         0.59        36.53        54.48        10.09 
TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-5084 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5702 
       40.70        10.29         7.30        58.59        52.87        71.41 
TCGA-B2-3923 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5158 
       32.61        12.00         5.10         5.46        25.55        40.04 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 
       89.36        64.27        21.21        11.31         5.98        13.15 
TCGA-BP-4770 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 
       10.82        15.78        36.39        87.45        71.41        58.68 
TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5175 
       57.40        46.45        16.47        43.00         6.35        30.64 
TCGA-BP-5180 TCGA-BP-5185 TCGA-CJ-4635 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 
       74.40        37.22        46.55        79.66        47.18        66.21 
TCGA-CJ-4887 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CJ-5679 
       30.64       109.84        47.67        49.28       133.71        22.32 
TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5452 
       53.42        66.31        25.45        69.21       107.41        58.82 
TCGA-CZ-5456 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-EU-5907 
       79.63        84.30         1.94        67.96        14.63         4.18 
TCGA-MM-A563 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-5P-A9KH TCGA-A4-7286 TCGA-B3-3926 
       19.43        54.64        51.52        67.43        18.21        29.03 
TCGA-BQ-5882 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 
       21.63        19.00        13.08         4.01        11.05        25.15 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 TCGA-P4-A5E8 TCGA-SX-A7SL 
       25.84        23.08         3.68        58.19        42.94        27.06 
TCGA-UN-AAZ9 TCGA-Y8-A896 
       18.02        18.64 

$`6P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 
       23.28        28.80        47.21        38.47        31.07        42.97 
TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 
       82.32       109.91        58.49        28.73        22.45        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
      111.02        94.72        80.68        54.77        77.62        44.15 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 
       48.10        49.15        27.02        44.55        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       26.93        27.65        53.26        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
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        81.21 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       16.18        22.49        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-DW-5560 
       11.97        96.92        44.84        26.27        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8477 
        6.74       109.22        71.41        28.80        62.37        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8433 
       31.33        23.47        25.91         3.55         0.99        11.21 
TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 
      100.87       103.10        99.88        12.66        11.90         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       39.16        24.16        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
       38.99        37.38        48.82        45.53        29.92        88.37 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 
       10.62       117.80       122.56       109.41        73.68        46.78 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 
       48.36        78.64        94.29        83.21        37.58        82.45 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       72.89         1.41         3.32         4.57         2.53        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72        46.59         5.52        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        10.52        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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       11.90        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       52.54        30.48        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
      131.15        89.49        91.46        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        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        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       17.19        50.14        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        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-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 
       62.86        49.08        44.94        12.23        31.89        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 
       31.33        12.30        72.59        77.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       48.07        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 
       68.38        60.95        48.95        36.53        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
        6.71        47.97        63.62        60.30        61.22         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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        31.30        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        3.88        46.45        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       37.48        35.21        28.87        79.30         2.04        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 
       52.27         9.63        38.30        42.44        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82        34.95         0.95       115.00        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       83.97        49.25        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4888 
       71.87        61.91        57.83       113.46        64.18        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       63.98       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       56.35        49.97        51.29        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       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
       72.00       129.40        25.71        18.87        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
      122.83        62.10        73.35        67.00        62.66       119.64 
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-6097 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       18.77        47.08        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       93.04        63.42        79.53        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       69.96        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       65.65        12.26        22.78        62.63        53.46        12.00 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
       18.12         3.91         6.77         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
        2.01        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       56.81        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
        5.29         0.13        12.82        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 
       43.04        19.36        12.99        12.39        27.09        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       33.83        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-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        90.90        39.25        71.44        20.52        25.25 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        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        53.10 
TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       43.76        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.59              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           153.73            194.79 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            43.10             33.47 
[1] "0.6 - 153.7 (43.1)" "0.1 - 194.8 (33.5)"
[1] "hr=" "1.1"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6P LOSS MUTATED        58       36        46       28
  6P LOSS WILD-TYPE     396       67       144       76
D52V3, multiclass
           clus
vv          6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                58               396
  STAGE II               36                67
  STAGE III              46               144
  STAGE IV               28                76
[1] 4 2
[1] TRUE
[1] "dimension of 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    61  39  66   5
  6P LOSS WILD-TYPE 419  88 192  10
D52V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1              61               419
  T2              39                88
  T3              66               192
  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    73  11   4
  6P LOSS WILD-TYPE 250  33   2
D52V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              73               250
  N1              11                33
  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 430  69
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED    116   20
  6P LOSS WILD-TYPE  430   69
   clus
vv  6P LOSS MUTATED 6P LOSS WILD-TYPE
  0             116               430
  1              20                69
[1] 2 2
[1] FALSE
D52V7, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    53 118
  6P LOSS WILD-TYPE 239 472
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     53  118
  6P LOSS WILD-TYPE  239  472
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              53               239
  MALE               118               472
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED    83   0
  6P LOSS WILD-TYPE 325   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     83    0
  6P LOSS WILD-TYPE  325    3
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO               83               325
  YES               0                 3
[1] 2 2
[1] FALSE
D52V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6P LOSS MUTATED                   50                               100
  6P LOSS WILD-TYPE                 16                               428
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6P LOSS MUTATED                                      21
  6P LOSS WILD-TYPE                                   267
D52V10, multiclass
                                       clus
vv                                      6P LOSS MUTATED 6P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 50                16
  KIDNEY CLEAR CELL RENAL CARCINOMA                 100               428
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              21               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"
D52V11, continuous
D52V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6P LOSS MUTATED                                  0     4
  6P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED                           8   152
  6P LOSS WILD-TYPE                       113   567
D52V13, multiclass
                                  clus
vv                                 6P LOSS MUTATED 6P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                      8               113
  WHITE                                        152               567
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V14, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     8 104
  6P LOSS WILD-TYPE  34 518
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      8  104
  6P LOSS WILD-TYPE   34  518
                        clus
vv                       6P LOSS MUTATED 6P LOSS WILD-TYPE
  HISPANIC OR LATINO                   8                34
  NOT HISPANIC OR LATINO             104               518
[1] 2 2
[1] FALSE

Clustering(53) Variable = 6Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  6Q LOSS MUTATED   154  51
  6Q LOSS WILD-TYPE 494 177
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
              205               671 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               51               177 
$`6Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3336 TCGA-B0-4707 
      102.81        28.11        47.24       130.13        34.29        19.73 
TCGA-B0-4712 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4775 
       43.96        32.61         3.58        74.17        12.33        60.59 
TCGA-BP-4986 TCGA-BP-5178 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4904 TCGA-CJ-6027 
       25.81        62.86        31.79        31.27       108.56       118.85 
TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 TCGA-G6-A8L7 TCGA-2Z-A9JJ TCGA-5P-A9JU 
       12.16        37.15        56.84        70.13        39.88        12.26 
TCGA-B9-A44B TCGA-BQ-5888 TCGA-BQ-7056 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       11.87        13.25        20.12        38.07       153.73        23.84 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       24.79        73.91        54.74       151.96        44.91        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       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
       92.71        16.67       104.55       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
       92.55        36.82        49.08        49.02        37.15        49.58 
TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3374 TCGA-A3-3380 
       62.01         4.50        52.93        18.44        43.20        18.64 
TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3426 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 
       18.87         0.10        29.10        15.78       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 
      109.51        94.19        40.01        38.40        12.13        40.70 
TCGA-B0-4690 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4810 
        1.41         3.48        28.47         1.38         3.62        15.72 
TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4844 TCGA-B0-4849 
       36.53        54.48        10.09        40.70        10.29         2.27 
TCGA-B0-5084 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 TCGA-B0-5702 
        7.30        58.59        52.87        51.02        42.41        71.41 
TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
       32.61        21.57        12.00         5.10         0.53         5.46 
TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4167 TCGA-BP-4176 
       49.97        25.55        40.04         1.74        89.36        64.27 
TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4352 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4770 
       97.45        21.21        11.31         5.98        13.15        10.82 
TCGA-BP-4777 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 
       56.91        15.78        36.39        87.45        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4992 TCGA-BP-4994 
       60.30        57.40        46.45        36.95        16.47        43.00 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5185 TCGA-CJ-4634 
       18.51         6.35        30.64        74.40        37.22       115.00 
TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 TCGA-CJ-4887 
       46.55        58.95        79.66        47.18        66.21        30.64 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-5675 
       24.66        39.45       109.84        47.67        49.28       129.40 
TCGA-CJ-5676 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CJ-6032 TCGA-CW-5584 TCGA-CW-5585 
      133.71        22.32        53.42       119.64         5.39        85.78 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4866 TCGA-CZ-5452 
       66.31        25.45        69.21        58.75       107.41        58.82 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5987 
       79.63        94.45        84.30        80.19        67.96        14.63 
TCGA-EU-5907 TCGA-MM-A563 TCGA-MW-A4EC TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
        4.18        19.43        16.37        91.73        54.64        51.52 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-B3-3926 TCGA-BQ-5875 TCGA-BQ-5882 TCGA-EV-5902 
       67.43        18.21        29.03        86.76        21.63        19.00 
TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 
       13.08         4.01        11.05        25.84        23.08         3.68 
TCGA-HE-7130 TCGA-J7-8537 TCGA-P4-A5EB TCGA-SX-A7SL TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       58.19        10.55        99.12        27.06        18.02        86.27 
TCGA-Y8-A896 
       18.64 

$`6Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 
       23.28        28.80        47.21        38.47        31.07        42.97 
TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 
       82.32       109.91        58.49        28.73        22.45        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
      111.02        94.72        80.68        54.77        77.62        44.15 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 
       48.10        49.15        27.02        44.55        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
       26.93        27.65        53.26        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        43.69        45.96        65.88 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 
       11.67        66.28        23.90        81.21        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV 
       34.85        33.07        25.58        16.18        22.49        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 
       21.67        27.68        21.07        10.16        21.86        19.23 
TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7058 
       26.04        11.97        96.92        44.84        26.27        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 
       15.62         6.74       109.22        71.41        28.80        62.37 
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-A3-3308 
      100.87       103.10        99.88        12.66        11.90         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
       39.16        24.16        48.59        36.36        38.99        37.38 
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       48.82        45.53        29.92        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       20.71        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 
       22.65         0.10        11.18        10.62       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 
      109.41        73.68        46.78        48.36        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       83.21        37.58        82.45        72.89         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-B0-4811 
        2.14        57.70         6.64         3.25        58.45        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 
       40.44        14.93        29.10        78.44        68.71        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 
       27.42        53.88         6.71        56.68        10.52        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07        29.03        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       38.63        52.73        41.88        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       80.91        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
      131.15        89.49        91.46        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 
       21.30        31.30        31.66        32.98        16.67         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         4.64         0.36         0.23        23.31        16.80 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5159 
       42.71        25.05        45.37        17.19        50.14        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       17.06         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       90.28       101.06        93.34        99.85         0.43        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 
       77.03        62.24        61.78        54.90        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       52.24        62.86        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 
       33.99        31.33        12.30        72.59        77.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       71.80        48.07        61.68         5.33        61.97        13.51 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 
       68.38        60.95        48.95        36.53        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 
        6.71        47.97        63.62        61.22         6.74        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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4989 TCGA-BP-4991 
       14.93        36.07        33.34        31.30         3.88        46.45 
TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       30.64        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 
       79.30         2.04        74.20        52.27         9.63        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       42.44        37.25        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4644 
       73.22        14.17       106.16       114.41        54.61        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        74.27        75.06       116.84 
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       113.46        64.18 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4899 TCGA-CJ-4900 
       51.52        63.98       115.69        50.01        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       131.08        72.00 
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       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       73.35        67.00        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-6097 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       83.90        18.77        47.08         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       93.04        63.42        79.53        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       91.69        55.33        10.85        10.22        21.76        69.96 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5985 
       22.52         2.40         1.94        31.10        12.69        65.65 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       12.26        22.78        62.63        53.46        12.00        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-A564 TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       19.96        11.70         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
      100.27        56.91         4.57        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       12.39        27.09        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        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-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       51.19        74.60        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        90.90        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
       25.15        20.52        25.25        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        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94         6.61        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       44.61        28.80        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.10              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           153.73            194.79 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            44.84             31.89 
[1] "0.1 - 153.7 (44.8)" "0.1 - 194.8 (31.9)"
[1] "hr=" "1.3"
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  6Q LOSS MUTATED        81       40        50       32
  6Q LOSS WILD-TYPE     373       63       140       72
D53V3, multiclass
           clus
vv          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                81               373
  STAGE II               40                63
  STAGE III              50               140
  STAGE IV               32                72
[1] 4 2
[1] TRUE
[1] "dimension of 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    83  43  73   7
  6Q LOSS WILD-TYPE 397  84 185   8
D53V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1              83               397
  T2              43                84
  T3              73               185
  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    83  15   4
  6Q LOSS WILD-TYPE 240  29   2
D53V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              83               240
  N1              15                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"
D53V6, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED   142  22
  6Q LOSS WILD-TYPE 404  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED    142   22
  6Q LOSS WILD-TYPE  404   67
   clus
vv  6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  0             142               404
  1              22                67
[1] 2 2
[1] FALSE
D53V7, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    72 134
  6Q LOSS WILD-TYPE 220 456
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     72  134
  6Q LOSS WILD-TYPE  220  456
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              72               220
  MALE               134               456
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    99   0
  6Q LOSS WILD-TYPE 309   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     99    0
  6Q LOSS WILD-TYPE  309    3
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO               99               309
  YES               0                 3
[1] 2 2
[1] FALSE
D53V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  6Q LOSS MUTATED                   51                               128
  6Q LOSS WILD-TYPE                 15                               400
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  6Q LOSS MUTATED                                      27
  6Q LOSS WILD-TYPE                                   261
D53V10, multiclass
                                       clus
vv                                      6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 51                15
  KIDNEY CLEAR CELL RENAL CARCINOMA                 128               400
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              27               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"
D53V11, continuous
D53V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  6Q LOSS MUTATED                                  0     6
  6Q LOSS WILD-TYPE                                2    10
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED                          13   179
  6Q LOSS WILD-TYPE                       108   540
D53V13, multiclass
                                  clus
vv                                 6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          6                10
  BLACK OR AFRICAN AMERICAN                     13               108
  WHITE                                        179               540
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V14, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    11 126
  6Q LOSS WILD-TYPE  31 496
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     11  126
  6Q LOSS WILD-TYPE   31  496
                        clus
vv                       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             126               496
[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 646 226
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                4               872 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                2               226 
$`7P LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-KL-8332 TCGA-B0-4698 TCGA-BP-4761 
       12.99        84.89         1.38         5.98 

$`7P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4699 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         3.62        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        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 
       33.99        31.33        12.30        72.59        77.98        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-4784 TCGA-BP-4787 
       61.97        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        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-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  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            35.915 
[1] "1.4 - 84.9 (9.5)"   "0.1 - 194.8 (35.9)"
[1] "hr=" "3.2"
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7P LOSS MUTATED         1        0         2        1
  7P LOSS WILD-TYPE     453      103       188      103
D54V3, multiclass
           clus
vv          7P LOSS MUTATED 7P LOSS WILD-TYPE
  STAGE I                 1               453
  STAGE II                0               103
  STAGE III               2               188
  STAGE IV                1               103
[1] 4 2
[1] TRUE
[1] "dimension of 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 478 127 257  14
D54V4, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  T1               2               478
  T2               0               127
  T3               1               257
  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 322  42   6
D54V5, multiclass
    clus
vv   7P LOSS MUTATED 7P LOSS WILD-TYPE
  N0               1               322
  N1               2                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"
D54V6, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     3   0
  7P LOSS WILD-TYPE 543  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      3    0
  7P LOSS WILD-TYPE  543   89
   clus
vv  7P LOSS MUTATED 7P LOSS WILD-TYPE
  0               3               543
  1               0                89
[1] 2 2
[1] FALSE
D54V7, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   4
  7P LOSS WILD-TYPE 292 586
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    4
  7P LOSS WILD-TYPE  292  586
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE               0               292
  MALE                 4               586
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     2   0
  7P LOSS WILD-TYPE 406   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      2    0
  7P LOSS WILD-TYPE  406    3
     clus
vv    7P LOSS MUTATED 7P LOSS WILD-TYPE
  NO                2               406
  YES               0                 3
[1] 2 2
[1] FALSE
D54V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7P LOSS MUTATED                    1                                 2
  7P LOSS WILD-TYPE                 65                               526
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7P LOSS MUTATED                                       1
  7P LOSS WILD-TYPE                                   287
D54V10, multiclass
                                       clus
vv                                      7P LOSS MUTATED 7P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               526
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
D54V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7P LOSS MUTATED                                  0     0
  7P LOSS WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED                           0     4
  7P LOSS WILD-TYPE                       121   715
D54V13, multiclass
                                  clus
vv                                 7P LOSS MUTATED 7P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                16
  BLACK OR AFRICAN AMERICAN                      0               121
  WHITE                                          4               715
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V14, binary
                   cls
clus                  0   1
  7P LOSS MUTATED     0   2
  7P LOSS WILD-TYPE  42 620
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED      0    2
  7P LOSS WILD-TYPE   42  620
                        clus
vv                       7P LOSS MUTATED 7P LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO               2               620
[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 646 226
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                4               872 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               226 
$`7Q LOSS MUTATED`
TCGA-A4-A5Y1 TCGA-KL-8332 TCGA-B0-4698 TCGA-BP-4761 
       12.99        84.89         1.38         5.98 

$`7Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       61.05        21.37         0.89        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
      100.87       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4699 TCGA-B0-4700 
        2.53         3.48        28.47        19.00         3.62        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        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 
       33.99        31.33        12.30        72.59        77.98        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-4784 TCGA-BP-4787 
       61.97        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97        87.45        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       16.47        43.00        30.64        18.51        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       37.48        35.21        28.87         6.35        79.30         2.04 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        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-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  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            35.915 
[1] "1.4 - 84.9 (9.5)"   "0.1 - 194.8 (35.9)"
[1] "hr=" "3.2"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  7Q LOSS MUTATED         1        0         2        1
  7Q LOSS WILD-TYPE     453      103       188      103
D55V3, multiclass
           clus
vv          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                 1               453
  STAGE II                0               103
  STAGE III               2               188
  STAGE IV                1               103
[1] 4 2
[1] TRUE
[1] "dimension of 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 478 127 257  14
D55V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               2               478
  T2               0               127
  T3               1               257
  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 322  42   6
D55V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               1               322
  N1               2                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"
D55V6, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     3   0
  7Q LOSS WILD-TYPE 543  89
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      3    0
  7Q LOSS WILD-TYPE  543   89
   clus
vv  7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  0               3               543
  1               0                89
[1] 2 2
[1] FALSE
D55V7, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   4
  7Q LOSS WILD-TYPE 292 586
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    4
  7Q LOSS WILD-TYPE  292  586
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               0               292
  MALE                 4               586
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   0
  7Q LOSS WILD-TYPE 406   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    0
  7Q LOSS WILD-TYPE  406    3
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                2               406
  YES               0                 3
[1] 2 2
[1] FALSE
D55V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  7Q LOSS MUTATED                    1                                 2
  7Q LOSS WILD-TYPE                 65                               526
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  7Q LOSS MUTATED                                       1
  7Q LOSS WILD-TYPE                                   287
D55V10, multiclass
                                       clus
vv                                      7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  1                65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   2               526
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               1               287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
D55V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  7Q LOSS MUTATED                                  0     0
  7Q LOSS WILD-TYPE                                2    16
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED                           0     4
  7Q LOSS WILD-TYPE                       121   715
D55V13, multiclass
                                  clus
vv                                 7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          0                16
  BLACK OR AFRICAN AMERICAN                      0               121
  WHITE                                          4               715
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V14, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   2
  7Q LOSS WILD-TYPE  42 620
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    2
  7Q LOSS WILD-TYPE   42  620
                        clus
vv                       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   0                42
  NOT HISPANIC OR LATINO               2               620
[1] 2 2
[1] FALSE

Clustering(56) Variable = 8P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  8P LOSS MUTATED   103  58
  8P LOSS WILD-TYPE 545 170
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
              161               715 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               58               170 
$`8P LOSS MUTATED`
TCGA-KO-8411 TCGA-A3-3325 TCGA-A3-3336 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 
      130.13        38.47        34.29       109.91        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5695 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4353 TCGA-BP-4775 
       52.21        70.68        32.61         3.58        12.33        60.59 
TCGA-BP-4782 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4986 TCGA-BP-5201 
       11.64        37.25         6.94        61.51        25.81        31.27 
TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
      105.37        27.65       108.56        53.26       118.85        75.58 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5574 TCGA-DV-5575 
       46.16       107.54         5.46        43.69        66.28        56.84 
TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-DW-5560 TCGA-SX-A7SO TCGA-KL-8327 TCGA-KL-8337 
       67.17        12.99        48.85        41.33       137.06        44.84 
TCGA-KM-8476 TCGA-KN-8432 TCGA-KN-8435 TCGA-KN-8436 TCGA-KO-8414 TCGA-KO-8416 
      123.12         2.50       115.00        42.35       105.60        90.48 
TCGA-KO-8417 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 
       92.55        37.15         4.50        28.70        24.16        53.29 
TCGA-A3-3382 TCGA-A3-A6NN TCGA-AK-3426 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       18.87         0.10        29.10        68.61       109.51        94.19 
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-B0-4718 TCGA-B0-4813 TCGA-B0-4816 TCGA-B0-4819 TCGA-B0-4822 
        5.98        58.45         0.59        45.07         6.02        36.53 
TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4845 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5094 
       40.70        27.42        65.29         2.27        70.52        10.95 
TCGA-B0-5102 TCGA-B0-5108 TCGA-B0-5696 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-A4SR 
       90.87        58.59        85.78        89.49        91.46        16.67 
TCGA-B4-5377 TCGA-B4-5838 TCGA-B8-4143 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-5158 
       12.00         5.46        23.31        49.97        42.71        40.04 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54I 
       27.02         0.85        50.14         6.38         0.53         4.93 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       61.78        64.27        53.42        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4781 TCGA-BP-4787 
       62.86        44.94        31.89        11.31        68.38        15.78 
TCGA-BP-4798 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       10.98        87.45        71.41         6.74        57.40        14.24 
TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5004 TCGA-BP-5173 TCGA-BP-5175 
       45.50        43.00        30.64        37.02         2.04        30.64 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5200 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 
        9.63        38.30        34.95       114.41        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4888 
       49.25        64.27        71.87        57.83       113.46        51.52 
TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5672 
       63.98       109.84        51.29        49.28        54.48        72.00 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6033 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4860 
       25.71        22.32         7.36       105.93        83.90         6.77 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       79.53        90.54        10.22        21.76        84.30        22.52 
TCGA-CZ-5468 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-G6-A8L8 TCGA-MM-A563 TCGA-2Z-A9J3 
        1.94        12.26        22.78        35.87        19.43        58.22 
TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-AL-3466 TCGA-B1-7332 TCGA-B3-3926 TCGA-BQ-5889 
       15.48        43.04         9.63        37.51        29.03        10.82 
TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-A8LC TCGA-G7-A8LD TCGA-UN-AAZ9 
       13.08         1.18        23.08        16.90        18.02 

$`8P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-A3-3307 
      102.81        28.11        23.28        28.80        47.24        47.21 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       31.07        42.97        82.32        58.49        28.73        22.45 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5698 TCGA-B0-5812 
       18.51       112.80       133.94        15.78       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 
       94.72        80.68        74.17        54.77        77.62        44.15 
TCGA-BP-4795 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       20.38        53.65        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CW-6093 TCGA-CZ-4856 
       31.79        44.55        63.25        26.93       103.43         0.59 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5576 
       45.96        65.88        12.16        11.67        37.15        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 
       33.07        25.58        16.18        22.49        12.26        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       11.28        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8329 
        6.74        38.07       153.73        23.84       109.22        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-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       30.25        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-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-8433 TCGA-KN-8434 TCGA-KN-8437 TCGA-KO-8403 
       87.12        19.33        11.21        59.08       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 
      103.10        99.88        96.62        12.66        11.90        36.82 
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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
       48.59        36.36        38.99        37.38        48.82        62.01 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 
      109.41        15.78        73.68       112.08        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
       78.64        94.29        83.21        37.58        82.45        72.89 
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-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4706 TCGA-B0-4710 
       19.00         1.38        65.10         7.82         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4817 
        6.64         3.25        15.72        46.59         5.52        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-B0-4837 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       78.44        68.71        45.30        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 
       10.52        10.29        39.45        26.07        29.03        36.85 
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-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       15.09         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5109 TCGA-B0-5110 
       62.89        90.48        52.54        30.48        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B2-3923 TCGA-B2-3924 
      105.37       130.65        79.89       131.15        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       21.57         5.75         5.10         1.25         0.53         4.64 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
        0.36         0.23        16.80        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 
       25.55        50.14        23.74        24.23        16.60        48.53 
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-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       62.24        54.90        97.45        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 
       21.21        15.62         0.07        49.08        12.23        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4789 TCGA-BP-4790 
       61.97        13.51        56.91        60.95        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4962 
       36.39        36.95         6.71        47.97        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 
       60.30        61.22        58.98        48.89        49.38         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5001 
       36.95         3.88        46.45        16.47        18.51        38.70 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       37.48        35.21        28.87         6.35        79.30        74.20 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       52.27        74.40        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 
      106.16        54.61        11.05        83.97        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 
       74.27        75.06       116.84        66.21        61.91        64.18 
TCGA-CJ-4887 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 
       30.64       115.69        50.01        24.66        39.45        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4913 
       56.35        47.67        49.97        49.18        50.33        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5675 
       45.14         3.06         4.57        18.81       131.08       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        18.87        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 
       73.35        67.00        53.42        62.66       119.64        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
       78.18        74.66         1.35        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       69.21        58.75        14.66        63.39        93.04       107.41 
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        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5467 TCGA-CZ-5469 
       55.33        94.45        10.85        69.96         2.40        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 
       12.69        80.19        67.96        65.65        14.63        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
        7.96        10.29         2.01        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
        7.04        75.55        59.01       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       67.43        18.21        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
        7.82         0.23        16.64        30.48        29.46        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
       67.73         2.20        41.13        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       86.76        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       47.80        21.63        40.83        26.04        30.28        25.35 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
       74.60        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        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  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 
            40.04             33.83 
[1] "0.1 - 137.1 (40.0)" "0.1 - 194.8 (33.8)"
[1] "hr=" "1.4"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8P LOSS MUTATED        69       21        38       28
  8P LOSS WILD-TYPE     385       82       152       76
D56V3, multiclass
           clus
vv          8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                69               385
  STAGE II               21                82
  STAGE III              38               152
  STAGE IV               28                76
[1] 4 2
[1] TRUE
[1] "dimension of 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    73  24  60   4
  8P LOSS WILD-TYPE 407 103 198  11
D56V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1              73               407
  T2              24               103
  T3              60               198
  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   9   0
  8P LOSS WILD-TYPE 262  35   6
D56V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              61               262
  N1               9                35
  N2               0                 6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V6, binary
                   cls
clus                  0   1
  8P LOSS MUTATED   116  28
  8P LOSS WILD-TYPE 430  61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED    116   28
  8P LOSS WILD-TYPE  430   61
   clus
vv  8P LOSS MUTATED 8P LOSS WILD-TYPE
  0             116               430
  1              28                61
[1] 2 2
[1] FALSE
D56V7, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    49 112
  8P LOSS WILD-TYPE 243 478
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     49  112
  8P LOSS WILD-TYPE  243  478
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              49               243
  MALE               112               478
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    51   0
  8P LOSS WILD-TYPE 357   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     51    0
  8P LOSS WILD-TYPE  357    3
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO               51               357
  YES               0                 3
[1] 2 2
[1] FALSE
D56V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8P LOSS MUTATED                   10                               135
  8P LOSS WILD-TYPE                 56                               393
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8P LOSS MUTATED                                      16
  8P LOSS WILD-TYPE                                   272
D56V10, multiclass
                                       clus
vv                                      8P LOSS MUTATED 8P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                 135               393
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              16               272
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
D56V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8P LOSS MUTATED                                  0     4
  8P LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED                          12   143
  8P LOSS WILD-TYPE                       109   576
D56V13, multiclass
                                  clus
vv                                 8P LOSS MUTATED 8P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     12               109
  WHITE                                        143               576
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V14, binary
                   cls
clus                  0   1
  8P LOSS MUTATED    11 104
  8P LOSS WILD-TYPE  31 518
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     11  104
  8P LOSS WILD-TYPE   31  518
                        clus
vv                       8P LOSS MUTATED 8P LOSS WILD-TYPE
  HISPANIC OR LATINO                  11                31
  NOT HISPANIC OR LATINO             104               518
[1] 2 2
[1] FALSE

Clustering(57) Variable = 8Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED    61  22
  8Q LOSS WILD-TYPE 587 206
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               83               793 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               22               206 
$`8Q LOSS MUTATED`
TCGA-KO-8411 TCGA-A3-3325 TCGA-BP-4353 TCGA-BP-4775 TCGA-BP-5201 TCGA-CJ-4642 
      130.13        38.47        12.33        60.59        31.27       105.37 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CZ-4862 TCGA-DV-5575 
       27.65       108.56        53.26        75.58       107.54        56.84 
TCGA-5P-A9JV TCGA-A4-A5Y1 TCGA-KL-8327 TCGA-KL-8337 TCGA-KM-8476 TCGA-KN-8432 
       67.17        12.99       137.06        44.84       123.12         2.50 
TCGA-KN-8436 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3365 TCGA-A3-3372 
       42.35       105.60        90.48        92.55        28.70        24.16 
TCGA-A3-3373 TCGA-A3-A6NN TCGA-AK-3426 TCGA-AK-3440 TCGA-AK-3458 TCGA-AS-3777 
       53.29         0.10        29.10        94.19        38.40        40.70 
TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4822 TCGA-B0-4845 TCGA-B0-4945 
        3.62        58.45         0.59        36.53        65.29        70.52 
TCGA-B0-5696 TCGA-B4-5838 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-BP-4338 
       85.78         5.46         0.85        50.14         6.38        93.99 
TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4781 
       18.48        62.86        44.94        31.89        11.31        68.38 
TCGA-BP-4787 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4994 
       15.78        71.41         6.74        57.40        45.50        43.00 
TCGA-BP-5004 TCGA-BP-5177 TCGA-BP-5200 TCGA-CJ-4640 TCGA-CJ-4876 TCGA-CJ-4885 
       37.02         9.63        34.95       114.41        64.27       113.46 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5679 
       51.52        63.98       109.84        51.29        49.28        22.32 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5463 
      105.93        83.90         6.77        79.53        90.54        21.76 
TCGA-CZ-5465 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-MM-A563 TCGA-5P-A9K8 TCGA-B1-7332 
       84.30        12.26        22.78        19.43        43.04        37.51 
TCGA-B3-3926 TCGA-BQ-5889 TCGA-F9-A7Q0 TCGA-G7-A8LC TCGA-UN-AAZ9 
       29.03        10.82        13.08        23.08        18.02 

$`8Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-A3-3307 
      102.81        28.11        23.28        28.80        47.24        47.21 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 
       34.29        31.07        42.97        82.32       109.91        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       28.73        22.45        19.73        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 
       77.62        44.15        11.64        20.38        37.25         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       61.51        53.65        25.81        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-6027 
       27.02        31.79        44.55        63.25        26.93       118.85 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
      103.43        46.16         0.59         5.46        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5576 
       65.88        12.16        11.67        37.15        66.28        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-A4-7288 
       33.07        25.58        16.18        22.49        12.26        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      109.22        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       96.95        92.55        30.25        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       44.91        49.97        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8434 
        0.99        52.27        87.12        19.33        11.21        59.08 
TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
      115.00       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8415 
       92.71        16.67       104.55       103.10        99.88        96.62 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        51.25        10.49 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.63        74.76        43.20        55.76        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4688 
       37.58        82.45        72.89        12.13         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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        6.64         3.25        15.72        46.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        40.44        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        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 
       39.45        26.07        29.03         2.27        36.85        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
      111.52       129.67        86.47       126.28        80.91        71.41 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       89.49        91.46        32.61        35.90         1.68        31.96 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
       21.30        31.30        31.66        32.98        21.57        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       12.00         5.75         5.10         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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
       23.74        27.02        24.23        16.60        48.53         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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
        0.07        52.24        49.08        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       13.51        56.91        60.95        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 
       10.98        36.95         6.71        47.97        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       58.68        60.30        61.22        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
       49.38         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       30.64        18.51        38.70        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       19.82         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-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-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
      115.69        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       47.67        49.97        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       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 
      129.40       133.71        25.71        18.87        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5454 
       63.39        93.04       107.41        63.42        58.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       18.44        79.63        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       10.22        69.96        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 
       12.69        80.19        67.96        65.65        14.63        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        7.96        10.29        35.87         2.01        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 
       22.26        78.64        15.48        71.80        62.93        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        30.28        25.35         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-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        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       25.15        20.52        25.84        25.25        17.98        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      125.29        37.35        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  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 
            44.84             34.19 
[1] "0.1 - 137.1 (44.8)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1.2"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  8Q LOSS MUTATED        37       12        20       11
  8Q LOSS WILD-TYPE     417       91       170       93
D57V3, multiclass
           clus
vv          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                37               417
  STAGE II               12                91
  STAGE III              20               170
  STAGE IV               11                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
  8Q LOSS MUTATED    39  12  30   2
  8Q LOSS WILD-TYPE 441 115 228  13
D57V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1              39               441
  T2              12               115
  T3              30               228
  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 LOSS MUTATED    32   4   0
  8Q LOSS WILD-TYPE 291  40   6
D57V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0              32               291
  N1               4                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"
D57V6, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    62  10
  8Q LOSS WILD-TYPE 484  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     62   10
  8Q LOSS WILD-TYPE  484   79
   clus
vv  8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  0              62               484
  1              10                79
[1] 2 2
[1] FALSE
D57V7, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    22  61
  8Q LOSS WILD-TYPE 270 529
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     22   61
  8Q LOSS WILD-TYPE  270  529
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              22               270
  MALE                61               529
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    31   0
  8Q LOSS WILD-TYPE 377   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     31    0
  8Q LOSS WILD-TYPE  377    3
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO               31               377
  YES               0                 3
[1] 2 2
[1] FALSE
D57V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  8Q LOSS MUTATED                    9                                65
  8Q LOSS WILD-TYPE                 57                               463
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  8Q LOSS MUTATED                                       9
  8Q LOSS WILD-TYPE                                   279
D57V10, multiclass
                                       clus
vv                                      8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  9                57
  KIDNEY CLEAR CELL RENAL CARCINOMA                  65               463
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               9               279
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
D57V12, continuous
[1] "Remove cluster labels:" "8Q LOSS MUTATED"       
clus
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                73 
       TCGA-DV-A4W0        TCGA-G6-A8L7        TCGA-MM-A84U        TCGA-2Z-A9JD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-DW-5561        TCGA-PJ-A5Z9        TCGA-UZ-A9PO        TCGA-UZ-A9PR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-Y8-A8RZ        TCGA-KL-8330        TCGA-KL-8335        TCGA-KL-8341 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KL-8345        TCGA-KM-8639        TCGA-KN-8433        TCGA-KO-8408 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-KO-8409        TCGA-A3-A8OV        TCGA-A3-A8OW        TCGA-AK-3445 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AK-3451        TCGA-B2-A4SR        TCGA-B8-5158        TCGA-B8-5550 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-T7-A92I        TCGA-2Z-A9J3        TCGA-2Z-A9J7        TCGA-2Z-A9J8 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-2Z-A9JI        TCGA-2Z-A9JN        TCGA-2Z-A9JO        TCGA-4A-A93W 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-4A-A93Y        TCGA-A4-A48D        TCGA-A4-A57E        TCGA-A4-A5Y0 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-AL-3472        TCGA-AL-7173        TCGA-B1-A654        TCGA-B9-4114 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-B9-4117        TCGA-B9-A69E        TCGA-DW-7963        TCGA-F9-A97G 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-6793        TCGA-G7-6795        TCGA-G7-7501        TCGA-G7-A8LB 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-G7-A8LD        TCGA-G7-A8LE        TCGA-GL-7773        TCGA-GL-A9DD 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-HE-A5NI        TCGA-IA-A40U        TCGA-MH-A854        TCGA-MH-A856 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-P4-A5E6        TCGA-P4-AAVK        TCGA-Q2-A5QZ        TCGA-SX-A71S 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A71U        TCGA-SX-A7SL        TCGA-SX-A7SM        TCGA-SX-A7SR 
"8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" "8Q LOSS WILD-TYPE" 
       TCGA-SX-A7SS        TCGA-UZ-A9PM        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 
"8Q LOSS WILD-TYPE" 
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  8Q LOSS MUTATED                                  0     1
  8Q LOSS WILD-TYPE                                2    15
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED                           6    75
  8Q LOSS WILD-TYPE                       115   644
D57V13, multiclass
                                  clus
vv                                 8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          1                15
  BLACK OR AFRICAN AMERICAN                      6               115
  WHITE                                         75               644
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V14, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     6  51
  8Q LOSS WILD-TYPE  36 571
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      6   51
  8Q LOSS WILD-TYPE   36  571
                        clus
vv                       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   6                36
  NOT HISPANIC OR LATINO              51               571
[1] 2 2
[1] FALSE

Clustering(58) Variable = 9P LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED   101  89
  9P LOSS WILD-TYPE 547 139
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
              190               686 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               89               139 
$`9P LOSS MUTATED`
TCGA-A3-3325 TCGA-AK-3425 TCGA-AK-3450 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       38.47       109.91        58.49        19.73        43.96        52.21 
TCGA-B0-5694 TCGA-BP-4164 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4782 TCGA-BP-4986 
       15.78        32.61        74.17        12.33        11.64        25.81 
TCGA-BP-4995 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 
       45.07        35.90        62.86        27.02        31.79        31.27 
TCGA-CJ-4891 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-DV-5576 
       26.93        53.26       118.85        75.58        46.16        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       81.21        70.13        23.01        39.88        12.99        49.25 
TCGA-BQ-5888 TCGA-BQ-7056 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 TCGA-KL-8343 
       13.25        20.12       153.73        23.84        84.89        71.41 
TCGA-KL-8346 TCGA-KN-8427 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8415 TCGA-A3-3306 
       62.37         0.99        42.35        10.68        96.62        36.82 
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 
       39.16        49.08        49.02        37.15         4.50        52.93 
TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3426 TCGA-AK-3436 TCGA-AK-3445 
       18.44        24.16        18.87        29.10       109.51        78.64 
TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4710 
       40.70         3.32         1.41         4.57         3.48        57.70 
TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4828 
       46.59        33.50         6.02        40.44        36.53        10.09 
TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5094 TCGA-B0-5095 
       40.70        56.68        65.29        29.03        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5107 TCGA-B0-5113 
        2.24        21.86        52.08        62.89        30.48        38.63 
TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 
       41.88        48.82        42.41        80.91        31.66        21.57 
TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 
        5.10         5.46        25.55        50.14        40.04         6.38 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4343 TCGA-BP-4351 
        0.53        90.28        89.36        64.27        62.86        31.89 
TCGA-BP-4352 TCGA-BP-4763 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4797 
       11.31        41.75        48.07        13.15        68.38        36.39 
TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       10.98         6.71        71.41        58.68        60.30        61.22 
TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5169 
       45.50        31.30        43.00        18.51        28.87         6.35 
TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 
       30.64        74.40        42.44        33.47        19.82        46.55 
TCGA-CJ-4638 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4895 
       14.17        79.66        66.21        51.52       115.69        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       131.08       133.71        25.71        22.32        25.25 
TCGA-CJ-5682 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 
      122.83        53.42        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-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
       79.63        10.85        10.22        84.30        22.52         1.94 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-G6-A5PC TCGA-MM-A563 
       31.10        67.96        65.65        14.63         7.96        19.43 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7287 
       54.64        51.52        12.82        19.36        18.21        19.63 
TCGA-A4-A57E TCGA-AL-3466 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5879 
        8.48         9.63        29.03        20.61        14.86        22.92 
TCGA-BQ-5889 TCGA-BQ-7048 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       10.82        93.34        79.86        13.08         4.01        11.05 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-HE-7130 TCGA-IA-A40Y 
       71.44        20.52        23.08        16.90        58.19         2.04 
TCGA-J7-8537 TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       10.55        18.02        86.27        18.64 

$`9P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3454 
       47.21        34.29        31.07        42.97        82.32        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
       22.45        18.51       112.80       133.94        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 
      111.02        94.72         3.58        80.68        54.77        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       44.15        60.59        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 
       53.65        27.22         5.82        41.62        27.62        48.10 
TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 
       49.15        44.55        63.25       105.37        27.65       108.56 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
      103.43         0.59       107.54         5.46        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-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       75.42        34.85        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       19.23        26.04        11.97        96.92        44.84        26.27 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 
       15.91        15.62         6.74        38.07       109.22       137.06 
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-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       28.80        54.74       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-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-8437 
       19.33         2.50        11.21        59.08       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
      105.47       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
      103.10        99.88       105.60        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       11.90         0.53        24.16        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3349 TCGA-A3-3351 
       38.99        37.38        48.82        62.01        45.53        29.92 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3383 
       53.29        43.20        55.76        20.71        18.64        28.31 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
       15.78        73.68       112.08        68.61        94.19        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       48.36        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4696 
       82.45        72.89        12.13         1.41         2.53        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        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
        5.52        45.07        16.77        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-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 
       10.52        10.29        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-B0-5092 TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       25.32        15.09        15.95        90.87        90.48        52.54 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
       58.59        19.30        66.05        52.73        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       38.43        46.39        56.98       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47       126.28        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 
       35.90         1.68        31.96        21.30        31.30        32.98 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
       16.67        12.00         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        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.05        45.37        17.19        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
       24.23        50.14        16.60        48.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       16.27        14.17        85.51       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 
        0.43        23.05        77.03        62.24        61.78        54.90 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
       97.45        53.42        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-4346 
       15.62         0.07        93.99        18.48        52.24        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-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 
       77.98         5.98        71.80        61.68        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       61.97        13.51        56.91        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4967 
       36.53        36.95        47.97        87.45        63.62         6.74 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 
       57.40        58.98        14.24        48.89        49.38         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 
        3.88        46.45        16.47        30.64        38.70        37.02 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       37.48        35.21        79.30         2.04        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        9.63        38.30        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 
       33.24        23.47        13.41        24.62        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
      115.00        73.22       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        83.97        49.25        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
       75.06       116.84        64.27        71.87        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 
      113.46        64.18        30.64        63.98        50.01        24.66 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4916 
      109.84        50.24        49.97        51.29        49.18        45.14 
TCGA-CJ-4918 TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5681 
        3.06        18.81        72.00       129.40        18.87        18.15 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
       62.10        73.35        67.00       119.64        92.02        81.83 
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-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       25.45        58.75        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
       63.42        58.82        79.53        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 
       91.69        55.33        94.45        21.76        69.96         2.40 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       12.69        80.19        12.26        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
       12.00        18.12         3.91         6.77         4.18        10.29 
TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
       35.87         2.01        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7583 
       43.04        12.99        12.39        27.09        67.43         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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-3467 TCGA-AL-3471 TCGA-AL-3472 
       15.75         8.28        12.46        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       20.25        16.77        20.32        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06        17.23         0.16        17.49        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-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5890 
       21.63        40.83        26.04        30.28        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 
        0.95         7.92         2.76       123.62        48.26        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        80.88        51.19        74.60        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 
       90.90        39.25        25.15        25.84        25.25        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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
       12.43        12.89        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.53              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           153.73            194.79 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            36.46             35.54 
[1] "0.5 - 153.7 (36.5)" "0.1 - 194.8 (35.5)"
[1] "hr=" "2.5"
D58V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9P LOSS MUTATED        64       15        64       44
  9P LOSS WILD-TYPE     390       88       126       60
D58V3, multiclass
           clus
vv          9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                64               390
  STAGE II               15                88
  STAGE III              64               126
  STAGE IV               44                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
  9P LOSS MUTATED    69  22  94   7
  9P LOSS WILD-TYPE 411 105 164   8
D58V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1              69               411
  T2              22               105
  T3              94               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
  9P LOSS MUTATED    71  19   3
  9P LOSS WILD-TYPE 252  25   3
D58V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              71               252
  N1              19                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"
D58V6, binary
                   cls
clus                  0   1
  9P LOSS MUTATED   124  38
  9P LOSS WILD-TYPE 422  51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED    124   38
  9P LOSS WILD-TYPE  422   51
   clus
vv  9P LOSS MUTATED 9P LOSS WILD-TYPE
  0             124               422
  1              38                51
[1] 2 2
[1] FALSE
D58V7, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    57 135
  9P LOSS WILD-TYPE 235 455
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     57  135
  9P LOSS WILD-TYPE  235  455
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              57               235
  MALE               135               455
[1] 2 2
[1] FALSE
D58V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    59   1
  9P LOSS WILD-TYPE 349   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     59    1
  9P LOSS WILD-TYPE  349    2
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO               59               349
  YES               1                 2
[1] 2 2
[1] FALSE
D58V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9P LOSS MUTATED                   10                               149
  9P LOSS WILD-TYPE                 56                               379
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9P LOSS MUTATED                                      33
  9P LOSS WILD-TYPE                                   255
D58V10, multiclass
                                       clus
vv                                      9P LOSS MUTATED 9P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 10                56
  KIDNEY CLEAR CELL RENAL CARCINOMA                 149               379
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              33               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"
D58V11, continuous
D58V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9P LOSS MUTATED                                  0     3
  9P LOSS WILD-TYPE                                2    13
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED                          14   170
  9P LOSS WILD-TYPE                       107   549
D58V13, multiclass
                                  clus
vv                                 9P LOSS MUTATED 9P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          3                13
  BLACK OR AFRICAN AMERICAN                     14               107
  WHITE                                        170               549
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V14, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     7 133
  9P LOSS WILD-TYPE  35 489
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      7  133
  9P LOSS WILD-TYPE   35  489
                        clus
vv                       9P LOSS MUTATED 9P LOSS WILD-TYPE
  HISPANIC OR LATINO                   7                35
  NOT HISPANIC OR LATINO             133               489
[1] 2 2
[1] FALSE

Clustering(59) Variable = 9Q LOSS MUTATION ANALYSIS
D59V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED   107  86
  9Q LOSS WILD-TYPE 541 142
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
              193               683 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               86               142 
$`9Q LOSS MUTATED`
TCGA-A3-3325 TCGA-AK-3425 TCGA-AK-3450 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       38.47       109.91        58.49        19.73        43.96        52.21 
TCGA-B0-5694 TCGA-BP-4164 TCGA-BP-4342 TCGA-BP-4353 TCGA-BP-4782 TCGA-BP-4986 
       15.78        32.61        74.17        12.33        11.64        25.81 
TCGA-BP-4995 TCGA-BP-5009 TCGA-BP-5178 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 
       45.07        35.90        62.86        27.02        31.79        31.27 
TCGA-CJ-4891 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-DV-5576 TCGA-DV-A4W0 
       26.93        53.26       118.85        75.58        23.90        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B 
       70.13        23.01        39.88        12.99        49.25        11.87 
TCGA-BQ-5888 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8332 
       13.25        26.27        20.12       153.73        23.84        84.89 
TCGA-KL-8343 TCGA-KL-8346 TCGA-KN-8427 TCGA-KN-8436 TCGA-KO-8404 TCGA-KO-8408 
       71.41        62.37         0.99        42.35        10.68        16.67 
TCGA-KO-8415 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
       96.62        36.82        39.16        49.08        49.02        37.15 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3352 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3426 
        4.50        52.93        18.44        24.16        18.87        29.10 
TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3456 TCGA-AS-3777 TCGA-B0-4690 TCGA-B0-4691 
      109.51        78.64        37.58        40.70         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4821 
        3.48        57.70        46.59        33.50         6.02        40.44 
TCGA-B0-4822 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4848 
       36.53        10.09        40.70        56.68        65.29        29.03 
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-B0-5107 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5701 
       30.48        38.63        41.88        42.41        85.78        80.91 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 
       31.66        21.57         5.10         5.46        25.55        50.14 
TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 
       40.04         6.38         0.53        90.28        89.36        64.27 
TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4781 
       62.86        31.89        11.31        41.75        13.15        68.38 
TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 
       15.78        36.39        10.98         6.71        71.41        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 TCGA-BP-5000 
       60.30        61.22        45.50        31.30        43.00        18.51 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5196 
       28.87         6.35        30.64        74.40        42.44        33.47 
TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4873 
       19.82        46.55        14.17        21.24        79.66        74.27 
TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4888 TCGA-CJ-4890 TCGA-CJ-4895 TCGA-CJ-4900 
       64.27        66.21        51.52       115.69        39.45        56.35 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4920 
       47.67        49.28        50.33        54.48        38.56         4.57 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 
      131.08       133.71        25.71        22.32        25.25       122.83 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5584 TCGA-CW-5588 
       53.42        62.66         7.36        64.57         5.39        66.31 
TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5452 
       83.90        18.77        47.08        69.21         6.77        58.82 
TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 
       79.63        10.85        10.22        84.30        22.52        31.10 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-MM-A563 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       67.96        65.65        14.63        19.43        54.64        51.52 
TCGA-4A-A93X TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B3-3926 
       12.82        19.36        18.21        19.63         9.63        29.03 
TCGA-B3-4104 TCGA-B9-A69E TCGA-BQ-5879 TCGA-BQ-5889 TCGA-BQ-7048 TCGA-DZ-6131 
       34.49        14.86        22.92        10.82        93.34        79.86 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 
       10.68        13.08         4.01        11.05        71.44        20.52 
TCGA-G7-A8LC TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-J7-A8I2 TCGA-UN-AAZ9 
       23.08        58.19         2.04        10.55        10.09        18.02 
TCGA-Y8-A896 
       18.64 

$`9Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3454 
       47.21        34.29        31.07        42.97        82.32        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
       22.45        18.51       112.80       133.94        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4344 TCGA-BP-4760 
      111.02        94.72         3.58        80.68        54.77        77.62 
TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       44.15        60.59        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 
       53.65        27.22         5.82        41.62        27.62        48.10 
TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 
       49.15        44.55        63.25       105.37        27.65       108.56 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      103.43        46.16         0.59       107.54         5.46        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-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       56.84        75.42        34.85        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       76.64        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7058 
       19.23        26.04        11.97        96.92        44.84        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       15.62         6.74        38.07       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
      108.62        98.96        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-8344 
       44.84        86.56        66.54        24.79        73.91        28.80 
TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       54.74       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-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-8437 TCGA-KO-8403 
        2.50        11.21        59.08       115.00       100.87       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      100.47       103.40        92.71       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 
      105.60        90.48        92.55        12.66        11.90         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-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 
       48.82        62.01        45.53        29.92        88.37        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-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
       55.76        20.71        18.64        28.31        65.52        20.28 
TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        15.39        22.65         0.10         0.10        11.18 
TCGA-A3-A8OW TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       10.62       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
      112.08        68.61        94.19        46.78        48.36        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       94.29        83.21        38.40        82.45        72.89        12.13 
TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4693 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
        1.41         3.32         2.53        28.47        19.00         1.38 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 
        3.62        65.10         7.82         5.98         2.14         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72         0.59         5.52        45.07 
TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4834 
       16.77        14.93        54.48        29.10        78.44        68.71 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 
       45.30        27.42        53.88         6.71        10.52        10.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       39.45        26.07         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       15.95        90.87        90.48        52.54        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       66.05        52.73        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5699 
       46.39        56.98       111.52       129.67        86.47       126.28 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
       31.96        21.30        31.30        32.98        16.67        12.00 
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        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       17.19        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       16.60        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 
       85.51       101.06        93.34        99.85         0.43        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 
       27.78        62.07        37.25        21.21        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       93.99        18.48        52.24        49.08        44.94        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-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-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 
       13.51        56.91        60.95        48.95        36.53        36.95 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       47.97        87.45        63.62         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       14.24        48.89        49.38         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       16.47        30.64        38.70        37.02        37.48        35.21 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 
       79.30         2.04        74.20        52.27         9.63        38.30 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 
       13.41        24.62        34.95         0.95       115.00        73.22 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 
      106.16       114.41        54.61        58.95        11.05        83.97 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 
       49.25        47.18        75.06       116.84        71.87        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4892 
       57.83       113.46        64.18        30.64        63.98        50.01 
TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       24.66       109.84        50.24        49.97        51.29        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       129.40        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       119.64        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-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
      105.93        25.45        58.75        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 
      107.41        63.42        79.53        23.74        18.44        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 
       91.69        55.33        94.45        21.76        69.96         2.40 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
        1.94        12.69        80.19        12.26        22.78        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC 
        7.96        10.29        35.87         2.01        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        91.73        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        43.04        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       67.43         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       33.83        30.58        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
        0.16        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-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
      123.62        48.26        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        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        90.90        39.25        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-KV-A6GD TCGA-KV-A6GE 
       22.26        21.34        12.36        12.76        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       78.90        14.07        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.53              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           153.73            194.79 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            36.39             35.87 
[1] "0.5 - 153.7 (36.4)" "0.1 - 194.8 (35.9)"
[1] "hr=" "2.3"
D59V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  9Q LOSS MUTATED        63       19        67       42
  9Q LOSS WILD-TYPE     391       84       123       62
D59V3, multiclass
           clus
vv          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                63               391
  STAGE II               19                84
  STAGE III              67               123
  STAGE IV               42                62
[1] 4 2
[1] TRUE
[1] "dimension of 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    67  23  99   6
  9Q LOSS WILD-TYPE 413 104 159   9
D59V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1              67               413
  T2              23               104
  T3              99               159
  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    74  18   3
  9Q LOSS WILD-TYPE 249  26   3
D59V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              74               249
  N1              18                26
  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"
D59V6, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED   129  36
  9Q LOSS WILD-TYPE 417  53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED    129   36
  9Q LOSS WILD-TYPE  417   53
   clus
vv  9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  0             129               417
  1              36                53
[1] 2 2
[1] FALSE
D59V7, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    57 138
  9Q LOSS WILD-TYPE 235 452
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     57  138
  9Q LOSS WILD-TYPE  235  452
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              57               235
  MALE               138               452
[1] 2 2
[1] FALSE
D59V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    59   1
  9Q LOSS WILD-TYPE 349   2
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     59    1
  9Q LOSS WILD-TYPE  349    2
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO               59               349
  YES               1                 2
[1] 2 2
[1] FALSE
D59V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  9Q LOSS MUTATED                   11                               150
  9Q LOSS WILD-TYPE                 55                               378
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  9Q LOSS MUTATED                                      34
  9Q LOSS WILD-TYPE                                   254
D59V10, multiclass
                                       clus
vv                                      9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 11                55
  KIDNEY CLEAR CELL RENAL CARCINOMA                 150               378
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              34               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"
D59V11, continuous
D59V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  9Q LOSS MUTATED                                  0     4
  9Q LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED                          14   172
  9Q LOSS WILD-TYPE                       107   547
D59V13, multiclass
                                  clus
vv                                 9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     14               107
  WHITE                                        172               547
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V14, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     9 132
  9Q LOSS WILD-TYPE  33 490
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      9  132
  9Q LOSS WILD-TYPE   33  490
                        clus
vv                       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   9                33
  NOT HISPANIC OR LATINO             132               490
[1] 2 2
[1] FALSE

Clustering(60) Variable = 10P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  10P LOSS MUTATED    92  40
  10P LOSS WILD-TYPE 556 188
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
               132                744 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                40                188 
$`10P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B0-4712 TCGA-BP-4164 
      102.81        28.11        47.24       130.13        43.96        32.61 
TCGA-BP-4342 TCGA-BP-4775 TCGA-BP-5201 TCGA-DV-5566 TCGA-5P-A9JU TCGA-A4-A5Y1 
       74.17        60.59        31.27        45.96        12.26        12.99 
TCGA-AL-A5DJ TCGA-B9-A44B TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 
       49.25        11.87        38.07        23.84       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       71.41        54.74        62.37        44.91        49.97       123.12 
TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8428 
      129.37        87.91        25.48        65.19       104.52        52.27 
TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 
       87.12         2.50        59.08       115.00       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 
      100.47       103.40        92.71        16.67       104.55       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3346 TCGA-A3-3352 TCGA-A3-3374 
       96.62        90.48        92.55         4.50        18.44        43.20 
TCGA-A3-3380 TCGA-A3-A6NN TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 
       18.64         0.10       112.08        94.19        46.78        38.40 
TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4811 
       72.89        12.13         3.32        28.47         3.62        46.59 
TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-5117 TCGA-B2-3923 
        6.02        10.09        10.52        65.29        52.87        32.61 
TCGA-B2-5641 TCGA-B4-5835 TCGA-B8-4143 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4161 
       21.57         0.53        23.31         6.38        48.53        90.28 
TCGA-BP-4166 TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4770 
        0.43        21.21        62.86        31.89        11.31        10.82 
TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4985 TCGA-BP-4994 
       36.39         6.71        71.41        45.50        31.30        43.00 
TCGA-BP-5169 TCGA-BP-5173 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4874 
        6.35         2.04        33.47        19.82        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       109.84        47.67        49.28        18.81 
TCGA-CJ-5676 TCGA-CW-6090 TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 
      133.71        83.90         6.77        90.54        94.45        84.30 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-2Z-A9J8 
       31.10        12.69        80.19         4.18        35.87        91.73 
TCGA-5P-A9KH TCGA-AL-3466 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 
       67.43         9.63        20.61        19.27        21.63        79.86 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-Q2-A5QZ 
        4.01        20.52        25.84        23.08         3.68        14.07 

$`10P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       19.73        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42       111.02        94.72         3.58        80.68 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 
       54.77        12.33        77.62        44.15        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 
       62.86        49.15        27.02        31.79        44.55        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
       43.69        65.88        12.16        11.67        37.15        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M 
       67.17        61.05        21.37         0.89        76.64        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 
       27.68        21.07        10.16        21.86        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 
       15.91        15.62         6.74       153.73       109.22        28.80 
TCGA-KM-8438 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 
      151.96        51.06        31.33        23.47        25.91         3.55 
TCGA-KN-8427 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 
        0.99        19.33        11.21        42.35       100.87       103.10 
TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       99.88        12.66        11.90        36.82         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 
       36.36        38.99        37.38        48.82        62.01        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       45.53        29.92        88.37        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-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        15.39 
TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 TCGA-AK-3427 
       22.65         0.10        11.18        10.62        29.10       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
      122.56       109.41        15.78        73.68        68.61       109.51 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
       48.36        78.64        40.01        94.29        83.21        37.58 
TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       82.45        40.70         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        19.00         1.38        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        57.70         6.64         3.25        58.45        15.72 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 
        0.59         5.52        45.07        33.50        16.77        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-B0-4844 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-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       41.88        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 
       79.89       131.15        89.49        91.46        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR 
       31.96        21.30        31.30        31.66        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 
       12.00         5.75         5.10         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        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 
       27.02         0.85        24.23        50.14        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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4162 
        4.93        17.36        16.27        14.17        85.51       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-4329 
       61.78        64.27        54.90        97.45        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       62.07        37.25        15.62         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 
       52.24        49.08        44.94        12.23        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        13.15        61.68         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       10.98        36.95        47.97        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         6.74        57.40        58.98        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       48.89        49.38         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        46.45        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       28.87        79.30        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 
       13.35        33.24        23.47        13.41        24.62        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        74.27       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       66.21        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
       63.98       115.69        50.01        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-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06         4.57       131.08        72.00       129.40 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       23.74        18.44        79.63        91.69        55.33        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        69.96        22.52         2.40         1.94 
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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC 
       53.46        12.00        18.12         3.91         6.77         7.96 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       10.29         2.01        19.43        19.96        16.37        11.70 
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-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
        4.57        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 
       15.75         8.28        12.46        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
       34.49        12.46        50.50        28.18        26.40         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       17.49        12.30        86.76         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
       39.25        71.44        25.15        25.25        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-7129 TCGA-HE-7130 TCGA-HE-A5NH 
       12.89        11.21        16.31        81.93        58.19        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       11.84        56.75        73.25        25.22        16.80        19.99 
TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
        2.04        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       12.36        12.76        10.55        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 
       17.62        31.13        15.48        99.78        87.09        42.94 
TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM 
        6.61        99.12        92.58        52.27        16.01        50.60 
TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       78.90        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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 
             45.73              34.24 
[1] "0.1 - 137.1 (45.7)" "0.1 - 194.8 (34.2)"
[1] "hr=" "1"  
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10P LOSS MUTATED        42       27        43       19
  10P LOSS WILD-TYPE     412       76       147       85
D60V3, multiclass
           clus
vv          10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                 42                412
  STAGE II                27                 76
  STAGE III               43                147
  STAGE IV                19                 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
  10P LOSS MUTATED    44  29  55   5
  10P LOSS WILD-TYPE 436  98 203  10
D60V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1               44                436
  T2               29                 98
  T3               55                203
  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    67   6   3
  10P LOSS WILD-TYPE 256  38   3
D60V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               67                256
  N1                6                 38
  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    86  14
  10P LOSS WILD-TYPE 460  75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     86   14
  10P LOSS WILD-TYPE  460   75
   clus
vv  10P LOSS MUTATED 10P LOSS WILD-TYPE
  0               86                460
  1               14                 75
[1] 2 2
[1] FALSE
D60V7, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    46  87
  10P LOSS WILD-TYPE 246 503
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     46   87
  10P LOSS WILD-TYPE  246  503
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               46                246
  MALE                 87                503
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    73   0
  10P LOSS WILD-TYPE 335   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     73    0
  10P LOSS WILD-TYPE  335    3
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                73                335
  YES                0                  3
[1] 2 2
[1] FALSE
D60V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10P LOSS MUTATED                   48                                68
  10P LOSS WILD-TYPE                 18                               460
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10P LOSS MUTATED                                      17
  10P LOSS WILD-TYPE                                   271
D60V10, multiclass
                                       clus
vv                                      10P LOSS MUTATED 10P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  48                 18
  KIDNEY CLEAR CELL RENAL CARCINOMA                   68                460
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               17                271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
D60V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10P LOSS MUTATED                                  0     2
  10P LOSS WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED                          12   114
  10P LOSS WILD-TYPE                       109   605
D60V13, multiclass
                                  clus
vv                                 10P LOSS MUTATED 10P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                      12                109
  WHITE                                         114                605
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V14, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     8  74
  10P LOSS WILD-TYPE  34 548
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      8   74
  10P LOSS WILD-TYPE   34  548
                        clus
vv                       10P LOSS MUTATED 10P LOSS WILD-TYPE
  HISPANIC OR LATINO                    8                 34
  NOT HISPANIC OR LATINO               74                548
[1] 2 2
[1] FALSE

Clustering(61) Variable = 10Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  10Q LOSS MUTATED   108  48
  10Q LOSS WILD-TYPE 540 180
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
               156                720 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                48                180 
$`10Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B0-4712 TCGA-BP-4164 
      102.81        28.11        47.24       130.13        43.96        32.61 
TCGA-BP-4342 TCGA-BP-4775 TCGA-BP-5201 TCGA-CJ-4642 TCGA-DV-5565 TCGA-DV-5566 
       74.17        60.59        31.27       105.37        43.69        45.96 
TCGA-5P-A9JU TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-KL-8323 TCGA-KL-8325 
       12.26        12.99        49.25        11.87        38.07        23.84 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8440 
       24.79        73.91        71.41        54.74        62.37        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 
       49.97       123.12       129.37        87.91        25.48        65.19 
TCGA-KN-8425 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 
      104.52        52.27        87.12         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       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       104.55       105.60        96.62        90.48        92.55 
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       112.08        94.19        46.78        38.40        72.89 
TCGA-AK-3465 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4718 
       12.13         3.32         1.41        28.47         3.62        58.45 
TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4843 
       46.59         6.02        10.09        40.70        45.30        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-5099 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 
       10.29        65.29        15.95        52.87        42.41        73.84 
TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4143 
      105.37        32.61        21.57         0.53         5.46        23.31 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4166 TCGA-BP-4329 
        6.38        48.53        16.27        90.28         0.43        27.78 
TCGA-BP-4334 TCGA-BP-4343 TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4770 TCGA-BP-4797 
       21.21        62.86        31.89        48.07        10.82        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-5180 TCGA-BP-5185 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 
        2.04        74.40        37.22        33.47        19.82        46.55 
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       109.84        47.67 
TCGA-CJ-4907 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-6090 
       49.28        18.81       133.71       119.64         7.36        83.90 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 
        6.77        90.54        94.45        84.30        31.10        12.69 
TCGA-CZ-5982 TCGA-EU-5907 TCGA-G6-A8L8 TCGA-2Z-A9J8 TCGA-5P-A9KH TCGA-AL-3466 
       80.19         4.18        35.87        91.73        67.43         9.63 
TCGA-BQ-5876 TCGA-BQ-5882 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-7502 
       19.27        21.63        79.86         4.01        20.52        25.84 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-7130 TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UZ-A9PQ 
       23.08         3.68        58.19        10.55        14.07        86.27 

$`10Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       19.73        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42       111.02        94.72         3.58        80.68 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 
       54.77        12.33        77.62        44.15        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 
       62.86        49.15        27.02        31.79        44.55        63.25 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5567 
      103.43        46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7288 
       33.07        25.58        16.18        22.49        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       21.37         0.89        76.64        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 
       10.16        21.86        19.23        26.04        13.25        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8344 TCGA-KM-8438 TCGA-KM-8477 
        6.74       153.73       109.22        28.80       151.96        51.06 
TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8431 
       31.33        23.47        25.91         3.55         0.99        19.33 
TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E 
       11.21       100.87       103.10        99.88        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       36.82         0.53        39.16        24.16        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3335 
       49.58        48.59        36.36        38.99        37.38        62.01 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       52.93        45.53        29.92        88.37        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-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       20.71        18.87        28.31        65.52        20.28        33.47 
TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW TCGA-AK-3426 
       15.39        22.65         0.10        11.18        10.62        29.10 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
      117.80       122.56       109.41        15.78        73.68        68.61 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
      109.51        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 
       37.58        82.45        40.70         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
        3.48        19.00         1.38        65.10         7.82         5.98 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 
        2.14        57.70         6.64         3.25        15.72         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-B0-4833 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-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        52.08        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       56.98       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       80.91        71.41       149.16       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        31.66        32.98        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
        5.10         1.25         4.64         0.36         0.23        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       50.14        16.60         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A8YJ 
       29.88        17.06         1.74         4.93        17.36        14.17 
TCGA-BP-4159 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       85.51       101.06        93.34        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-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       53.42        62.07        37.25        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4352 
       18.48        52.24        49.08        44.94        12.23        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 
       41.75        71.80        13.15        61.68         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 
       36.53        10.98        36.95        47.97        87.45        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         6.74        57.40        58.98 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 
       14.24        48.89        49.38         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        46.45        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
       35.21        28.87        79.30        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 
        9.63        38.30        42.44        37.25        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 
       33.24        23.47        13.41        24.62        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 
       74.27       116.84        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 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       50.01        39.45        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-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
        4.57       131.08        72.00       129.40        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       67.00        53.42        62.66        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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35       105.93        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
       55.33        10.85        10.22        21.76        69.96        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40         1.94        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        18.12         3.91 
TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        6.77         7.96        10.29         2.01        19.43        19.96 
TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       16.37        11.70         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
      100.27        56.91         4.57        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 
       19.36        12.99        12.39        27.09        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 
        8.88        63.72        22.92        43.20        47.80        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       40.77        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        16.90        80.65       194.79        12.92 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD 
       22.26        21.34        12.36        12.76        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       27.06        11.93        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       53.10        43.76        18.02        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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 
             45.73              33.29 
[1] "0.1 - 137.1 (45.7)" "0.1 - 194.8 (33.3)"
[1] "hr=" "1"  
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  10Q LOSS MUTATED        51       32        49       24
  10Q LOSS WILD-TYPE     403       71       141       80
D61V3, multiclass
           clus
vv          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                 51                403
  STAGE II                32                 71
  STAGE III               49                141
  STAGE IV                24                 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
  10Q LOSS MUTATED    53  34  63   7
  10Q LOSS WILD-TYPE 427  93 195   8
D61V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1               53                427
  T2               34                 93
  T3               63                195
  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    74   9   3
  10Q LOSS WILD-TYPE 249  35   3
D61V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               74                249
  N1                9                 35
  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   105  17
  10Q LOSS WILD-TYPE 441  72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED    105   17
  10Q LOSS WILD-TYPE  441   72
   clus
vv  10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  0              105                441
  1               17                 72
[1] 2 2
[1] FALSE
D61V7, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    52 105
  10Q LOSS WILD-TYPE 240 485
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     52  105
  10Q LOSS WILD-TYPE  240  485
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               52                240
  MALE                105                485
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    84   0
  10Q LOSS WILD-TYPE 324   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     84    0
  10Q LOSS WILD-TYPE  324    3
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                84                324
  YES                0                  3
[1] 2 2
[1] FALSE
D61V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  10Q LOSS MUTATED                   49                                89
  10Q LOSS WILD-TYPE                 17                               439
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  10Q LOSS MUTATED                                      19
  10Q LOSS WILD-TYPE                                   269
D61V10, multiclass
                                       clus
vv                                      10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  49                 17
  KIDNEY CLEAR CELL RENAL CARCINOMA                   89                439
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               19                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"
D61V11, continuous
D61V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  10Q LOSS MUTATED                                  0     3
  10Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED                          13   135
  10Q LOSS WILD-TYPE                       108   584
D61V13, multiclass
                                  clus
vv                                 10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 13
  BLACK OR AFRICAN AMERICAN                      13                108
  WHITE                                         135                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"
D61V14, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     9  91
  10Q LOSS WILD-TYPE  33 531
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      9   91
  10Q LOSS WILD-TYPE   33  531
                        clus
vv                       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    9                 33
  NOT HISPANIC OR LATINO               91                531
[1] 2 2
[1] FALSE

Clustering(62) Variable = 11P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    26  16
  11P LOSS WILD-TYPE 622 212
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                42                834 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                16                212 
$`11P LOSS MUTATED`
TCGA-KL-8328 TCGA-B0-4707 TCGA-BP-5201 TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 
      102.81        19.73        31.27        98.96        54.74        49.97 
TCGA-KN-8427 TCGA-KN-8434 TCGA-KN-8436 TCGA-A3-3316 TCGA-AK-3465 TCGA-B0-4696 
        0.99        59.08        42.35        49.08        12.13        28.47 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-5084 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5838 
        6.02        36.53         7.30        71.41        21.57         5.46 
TCGA-BP-4352 TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-5173 TCGA-CW-5588 TCGA-CZ-5465 
       11.31        13.15        31.30         2.04        66.31        84.30 
TCGA-CZ-5469 TCGA-2Z-A9JG TCGA-4A-A93X TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7287 
       31.10        54.64        12.82        43.04        19.36        19.63 
TCGA-B1-7332 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-G7-6789 
       37.51        34.49        19.27         8.88        21.63         4.01 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-HE-7130 TCGA-IA-A40Y TCGA-Y8-A896 TCGA-Y8-A8S1 
       25.84        16.90        58.19         2.04        18.64        13.28 

$`11P LOSS WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
       28.11        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
       94.72        32.61         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       12.33        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 
       62.86        49.15        27.02        31.79        44.55        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       12.99        76.64        49.25        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       10.16        21.86        11.87        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 
      137.06        90.48       108.62        84.89        98.33        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       73.91        71.41        28.80        62.37       151.96        44.91 
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-8435 TCGA-KN-8437 
       87.12        19.33         2.50        11.21       115.00       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       92.55        12.66        11.90        36.82         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 
       37.58        38.40        82.45        72.89        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-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 
        0.59         5.52        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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       11.90        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       86.47       126.28        80.91        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       32.98        16.67        12.00         5.75         5.10         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        31.89        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97        87.45        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       58.68        60.30        61.22         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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
       74.20        30.64        52.27         9.63        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00       129.40       133.71        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15       122.83        62.10        73.35        67.00 
TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       53.42        62.66       119.64         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        69.96        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY 
       29.36         5.29         0.13        11.57       106.55        49.58 
TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 
       90.21        22.26        78.64        15.48        71.80        62.93 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       30.58        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        17.49        12.30        86.76        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
        7.04         7.17         3.81        40.77        79.86        80.88 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
       51.19        74.60        34.19        19.00        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
       13.08         2.40         1.18         0.43        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        23.08        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       81.93        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       26.01        39.06        18.64        18.05        25.28         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 
            23.735             36.510 
[1] "1.0 - 102.8 (23.7)" "0.1 - 194.8 (36.5)"
[1] "hr=" "2"  
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11P LOSS MUTATED        11       10        10        9
  11P LOSS WILD-TYPE     443       93       180       95
D62V3, multiclass
           clus
vv          11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                 11                443
  STAGE II                10                 93
  STAGE III               10                180
  STAGE IV                 9                 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
  11P LOSS MUTATED    11  10  20   1
  11P LOSS WILD-TYPE 469 117 238  14
D62V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1               11                469
  T2               10                117
  T3               20                238
  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   7   2
  11P LOSS WILD-TYPE 310  37   4
D62V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0               13                310
  N1                7                 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"
D62V6, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    21   5
  11P LOSS WILD-TYPE 525  84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     21    5
  11P LOSS WILD-TYPE  525   84
   clus
vv  11P LOSS MUTATED 11P LOSS WILD-TYPE
  0               21                525
  1                5                 84
[1] 2 2
[1] FALSE
D62V7, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    15  27
  11P LOSS WILD-TYPE 277 563
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     15   27
  11P LOSS WILD-TYPE  277  563
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               15                277
  MALE                 27                563
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    22   0
  11P LOSS WILD-TYPE 386   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     22    0
  11P LOSS WILD-TYPE  386    3
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                22                386
  YES                0                  3
[1] 2 2
[1] FALSE
D62V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11P LOSS MUTATED                    7                                18
  11P LOSS WILD-TYPE                 59                               510
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11P LOSS MUTATED                                      17
  11P LOSS WILD-TYPE                                   271
D62V10, multiclass
                                       clus
vv                                      11P LOSS MUTATED 11P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   7                 59
  KIDNEY CLEAR CELL RENAL CARCINOMA                   18                510
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               17                271
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
D62V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11P LOSS MUTATED                                  0     0
  11P LOSS WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED                           3    36
  11P LOSS WILD-TYPE                       118   683
D62V13, multiclass
                                  clus
vv                                 11P LOSS MUTATED 11P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       3                118
  WHITE                                          36                683
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V14, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     0  29
  11P LOSS WILD-TYPE  42 593
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      0   29
  11P LOSS WILD-TYPE   42  593
                        clus
vv                       11P LOSS MUTATED 11P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               29                593
[1] 2 2
[1] FALSE

Clustering(63) Variable = 11Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    31  21
  11Q LOSS WILD-TYPE 617 207
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                52                824 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                21                207 
$`11Q LOSS MUTATED`
TCGA-KL-8328 TCGA-AK-3425 TCGA-B0-4707 TCGA-BP-4986 TCGA-BP-5201 TCGA-B9-A44B 
      102.81       109.91        19.73        25.81        31.27        11.87 
TCGA-KL-8331 TCGA-KL-8345 TCGA-KM-8443 TCGA-KN-8427 TCGA-KN-8434 TCGA-KN-8436 
       98.96        54.74        49.97         0.99        59.08        42.35 
TCGA-A3-3316 TCGA-A3-3346 TCGA-AK-3465 TCGA-B0-4696 TCGA-B0-4819 TCGA-B0-4822 
       49.08         4.50        12.13        28.47         6.02        36.53 
TCGA-B0-5084 TCGA-B0-5702 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4352 
        7.30        71.41        21.57         5.10         5.46        11.31 
TCGA-BP-4768 TCGA-BP-4985 TCGA-BP-5173 TCGA-CW-5588 TCGA-CZ-5465 TCGA-CZ-5468 
       13.15        31.30         2.04        66.31        84.30         1.94 
TCGA-CZ-5469 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K9 TCGA-B1-7332 
       31.10        54.64        51.52        12.82        19.36        37.51 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-7044 
       19.27         8.88        21.63        10.82         7.66       123.62 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD TCGA-HE-7130 
        0.43         4.01        11.05        25.84        16.90        58.19 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-UZ-A9PQ TCGA-Y8-A896 
        2.04        10.55        86.27        18.64 

$`11Q LOSS WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
       28.11        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 
       38.47        34.29        31.07        42.97        82.32        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
       28.73        22.45        43.96        52.21        18.51       112.80 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      133.94        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       25.91         1.18         8.42        15.42       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       32.61         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
        6.94        61.51        53.65        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 
       41.62        27.62        35.90        48.10        62.86        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        31.79        44.55        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       62.37       151.96        44.91       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-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
      104.52         3.55        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 
       11.21       115.00       100.87       105.47        10.68       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      103.40        92.71        16.67       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
       36.82         0.53        39.16        24.16        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-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
       62.01        52.93        45.53        29.92        18.44        88.37 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-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-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 
        3.48        19.00         1.38         3.62        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        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4821 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        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
       38.43        48.82        46.39        56.98        42.41       111.52 
TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
      129.67        85.78        86.47       126.28        80.91        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.30        31.66        32.98        16.67        12.00         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        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        31.89        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
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-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-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-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        22.52         2.40 
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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       56.81        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        5.29         0.13        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-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-5887 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
       30.28        25.35         0.95         7.92         2.76        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
        2.40         1.18        51.78        90.90        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        20.52        25.25        17.98        23.08        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25        25.22        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R 
       52.27        16.01        50.60        78.90        14.07        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       31.73        26.01        39.06        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.43               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            123.62             194.79 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            20.650             36.835 
[1] "0.4 - 123.6 (20.6)" "0.1 - 194.8 (36.8)"
[1] "hr=" "2.1"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  11Q LOSS MUTATED        12        9        18       12
  11Q LOSS WILD-TYPE     442       94       172       92
D63V3, multiclass
           clus
vv          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                 12                442
  STAGE II                 9                 94
  STAGE III               18                172
  STAGE IV                12                 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
  11Q LOSS MUTATED    12  10  29   1
  11Q LOSS WILD-TYPE 468 117 229  14
D63V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1               12                468
  T2               10                117
  T3               29                229
  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  10   3
  11Q LOSS WILD-TYPE 305  34   3
D63V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               18                305
  N1               10                 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"
D63V6, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    28   7
  11Q LOSS WILD-TYPE 518  82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     28    7
  11Q LOSS WILD-TYPE  518   82
   clus
vv  11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  0               28                518
  1                7                 82
[1] 2 2
[1] FALSE
D63V7, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    15  37
  11Q LOSS WILD-TYPE 277 553
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     15   37
  11Q LOSS WILD-TYPE  277  553
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               15                277
  MALE                 37                553
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    25   0
  11Q LOSS WILD-TYPE 383   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     25    0
  11Q LOSS WILD-TYPE  383    3
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                25                383
  YES                0                  3
[1] 2 2
[1] FALSE
D63V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  11Q LOSS MUTATED                    7                                23
  11Q LOSS WILD-TYPE                 59                               505
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  11Q LOSS MUTATED                                      22
  11Q LOSS WILD-TYPE                                   266
D63V10, multiclass
                                       clus
vv                                      11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   7                 59
  KIDNEY CLEAR CELL RENAL CARCINOMA                   23                505
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               22                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"
D63V11, continuous
D63V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  11Q LOSS MUTATED                                  0     2
  11Q LOSS WILD-TYPE                                2    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED                           5    42
  11Q LOSS WILD-TYPE                       116   677
D63V13, multiclass
                                  clus
vv                                 11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                       5                116
  WHITE                                          42                677
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V14, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     1  36
  11Q LOSS WILD-TYPE  41 586
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      1   36
  11Q LOSS WILD-TYPE   41  586
                        clus
vv                       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               36                586
[1] 2 2
[1] FALSE

Clustering(64) Variable = 12P LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED     4   3
  12P LOSS WILD-TYPE 644 225
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 7                869 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 3                225 
$`12P LOSS MUTATED`
TCGA-BP-4775 TCGA-A4-A5Y1 TCGA-KO-8404 TCGA-KO-8408 TCGA-BP-4166 TCGA-CZ-5457 
       60.59        12.99        10.68        16.67         0.43        90.54 
TCGA-T7-A92I 
       11.70 

$`12P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 
       74.17        54.77        12.33        77.62        44.15        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       98.33        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
       66.54        24.79        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 
       65.19       104.52         3.55         0.99        52.27        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 
       19.33         2.50        11.21        59.08       115.00        42.35 
TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 
      100.87       105.47       100.47       103.40        92.71       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52        10.29 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
       65.29        39.45        26.07        29.03         2.27        36.85 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
       70.52        20.94        43.30        11.24        11.90         7.30 
TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       25.32        15.09        10.95         8.05         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       41.88        52.87        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        49.97        42.71        25.05        45.37 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       17.19        25.55        50.14        40.04        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        50.14        16.60         6.38        48.53 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       90.28       101.06        93.34        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       48.07        13.15        61.68        10.82         5.33        61.97 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-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-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-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       43.00        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       79.63        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        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        16.37         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       56.81        54.64        51.52        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       71.80        62.93        43.04        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
       66.71        62.66        67.73         2.20        41.13        37.51 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
       36.49        20.25        16.77        20.32        33.83        29.03 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
        0.16        14.86        17.49        12.30        86.76        19.27 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 
        8.88        63.72        22.92        43.20        47.80        21.63 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        1.18         0.43         4.01        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM 
       39.25        71.44        25.15        20.52        25.84        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       17.98        23.08        16.90        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       10.55        10.09        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ 
       92.58        52.27        16.01        50.60        78.90        14.07 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
       47.90        49.45        44.61        28.80        27.06        11.93 
TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       19.00        16.31        41.62        26.47        53.10        43.76 
TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN 
       18.02        26.20       117.40       103.63       125.29        37.35 
TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       98.96        86.27        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.05        25.28         6.02        13.28 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.43               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             90.54             194.79 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             12.99              35.93 
[1] "0.4 - 90.5 (13.0)"  "0.1 - 194.8 (35.9)"
[1] "hr=" "2.4"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12P LOSS MUTATED         2        0         4        1
  12P LOSS WILD-TYPE     452      103       186      103
D64V3, multiclass
           clus
vv          12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                  2                452
  STAGE II                 0                103
  STAGE III                4                186
  STAGE IV                 1                103
[1] 4 2
[1] TRUE
[1] "dimension of 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     3   0   3   1
  12P LOSS WILD-TYPE 477 127 255  14
D64V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                3                477
  T2                0                127
  T3                3                255
  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 322  42   6
D64V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                1                322
  N1                2                 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"
D64V6, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     3   0
  12P LOSS WILD-TYPE 543  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      3    0
  12P LOSS WILD-TYPE  543   89
   clus
vv  12P LOSS MUTATED 12P LOSS WILD-TYPE
  0                3                543
  1                0                 89
[1] 2 2
[1] FALSE
D64V7, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     2   5
  12P LOSS WILD-TYPE 290 585
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      2    5
  12P LOSS WILD-TYPE  290  585
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE                2                290
  MALE                  5                585
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     4   0
  12P LOSS WILD-TYPE 404   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      4    0
  12P LOSS WILD-TYPE  404    3
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 4                404
  YES                0                  3
[1] 2 2
[1] FALSE
D64V9, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                141 
        TCGA-KM-8439         TCGA-KM-8441         TCGA-KM-8442 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-CZ-4854         TCGA-CZ-4856 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-DV-5565         TCGA-DV-5566 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4W0         TCGA-G6-A8L7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8440         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-KN-8429         TCGA-KN-8434         TCGA-KO-8413 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3428 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AK-3430         TCGA-B0-4838         TCGA-B2-5639 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4622         TCGA-B8-5158 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CZ-4858         TCGA-CZ-4860 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-5456         TCGA-CZ-5458 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DV-A4VX         TCGA-DV-A4VZ         TCGA-EU-5904 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L8         TCGA-2Z-A9JE 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JN         TCGA-4A-A93W 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-4A-A93X         TCGA-4A-A93Y         TCGA-A4-7286 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-7828         TCGA-A4-8098         TCGA-A4-8310 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-8311         TCGA-A4-8312         TCGA-A4-8517 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-8518         TCGA-A4-8630         TCGA-A4-A48D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-A4ZT         TCGA-A4-A57E         TCGA-A4-A5DU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-A5XZ         TCGA-A4-A6HP         TCGA-AL-3466 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-EV-5901         TCGA-EV-5902 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-EV-5903         TCGA-F9-A7Q0         TCGA-G7-6789 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-6790         TCGA-G7-6792         TCGA-G7-6793 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-6796         TCGA-G7-6797 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-7502         TCGA-G7-A4TM 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LC         TCGA-G7-A8LD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-IA-A40U         TCGA-IA-A40X 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IA-A40Y         TCGA-J7-8537         TCGA-P4-AAVK 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-Q2-A5QZ         TCGA-SX-A71R         TCGA-SX-A71S 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A71V         TCGA-SX-A7SL 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SM         TCGA-SX-A7SN         TCGA-SX-A7SP 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-UZ-A9PL         TCGA-V9-A7HT 
"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                                 4
  12P LOSS WILD-TYPE                 64                               524
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12P LOSS MUTATED                                       1
  12P LOSS WILD-TYPE                                   287
D64V10, multiclass
                                       clus
vv                                      12P LOSS MUTATED 12P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                    4                524
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                104 
        TCGA-B8-4621         TCGA-DV-A4W0         TCGA-G6-A8L7 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-KL-8324         TCGA-KL-8330 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8341         TCGA-KL-8345 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416         TCGA-A3-A8CQ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-4146 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-5550 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-G6-A5PC 
"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-A9JI 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JK         TCGA-2Z-A9JM         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-5P-A9K3         TCGA-5P-A9KE         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-B9-4114         TCGA-B9-4115 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-7268         TCGA-B9-A69E 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6792 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         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-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83V         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-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-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 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
D64V12, continuous
[1] "Remove cluster labels:" "12P LOSS MUTATED"      
clus
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 2                 72 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5550         TCGA-MM-A563 
"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-A9JI         TCGA-2Z-A9JN         TCGA-2Z-A9JO 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93Y         TCGA-A4-A48D 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-A4-A57E         TCGA-A4-A5Y0         TCGA-AL-3472 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-B9-4117         TCGA-B9-A69E         TCGA-DW-7963 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-F9-A97G         TCGA-G7-6793         TCGA-G7-6795 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"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-A9PS 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" "12P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"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    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED                           1     6
  12P LOSS WILD-TYPE                       120   713
D64V13, multiclass
                                  clus
vv                                 12P LOSS MUTATED 12P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       1                120
  WHITE                                           6                713
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V14, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     0   5
  12P LOSS WILD-TYPE  42 617
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      0    5
  12P LOSS WILD-TYPE   42  617
                        clus
vv                       12P LOSS MUTATED 12P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO                5                617
[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 645 227
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                872 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                227 
$`12Q LOSS MUTATED`
TCGA-BP-4775 TCGA-KO-8404 TCGA-BP-4166 TCGA-CZ-5457 
       60.59        10.68         0.43        90.54 

$`12Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 
       74.17        54.77        12.33        77.62        44.15        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 
       86.56        66.54        24.79        73.91        71.41        28.80 
TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 
       25.91        65.19       104.52         3.55         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 
       42.35       100.87       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
      109.51        94.19        46.78        48.36        78.64        40.01 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       94.29        83.21        37.58        38.40        82.45        72.89 
TCGA-AK-3465 TCGA-AS-3777 TCGA-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-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
        6.38        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       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-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 
       78.18        74.66         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
       25.45        47.08        69.21        58.75         6.77        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        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-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       56.91         4.57        91.73        56.81        54.64        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 
       19.36        12.99        12.39        27.09        67.43        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
       20.32        33.83        29.03        30.58        34.49        12.46 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
       50.50        28.18        26.40        20.61         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       12.30        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       43.20        47.80        21.63        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
       51.78        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
       80.65       194.79        12.92         3.68        27.65         1.05 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.43               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             90.54             194.79 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            35.635             35.900 
[1] "0.4 - 90.5 (35.6)"  "0.1 - 194.8 (35.9)"
[1] "hr=" "1"  
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  12Q LOSS MUTATED         1        0         2        1
  12Q LOSS WILD-TYPE     453      103       188      103
D65V3, multiclass
           clus
vv          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                  1                453
  STAGE II                 0                103
  STAGE III                2                188
  STAGE IV                 1                103
[1] 4 2
[1] TRUE
[1] "dimension of 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 479 127 256  14
D65V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                479
  T2                0                127
  T3                2                256
  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 322  44   6
D65V5, multiclass
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                372 
        TCGA-KL-8328         TCGA-KL-8339         TCGA-KN-8430 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3307         TCGA-A3-3343         TCGA-A3-3358 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3359         TCGA-AK-3425         TCGA-AK-3450 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5088         TCGA-B0-5691         TCGA-B0-5694 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5695         TCGA-B0-5698         TCGA-B8-4621 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-A54H         TCGA-BP-4158         TCGA-BP-4160 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4327         TCGA-BP-4331         TCGA-BP-4342 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4353         TCGA-BP-4795         TCGA-BP-4799 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4986         TCGA-BP-4988         TCGA-BP-4995 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5006         TCGA-BP-5191         TCGA-BP-5199 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5201         TCGA-CJ-4636         TCGA-CJ-4891 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4894         TCGA-CJ-4904         TCGA-CJ-6030 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4854         TCGA-CZ-4856         TCGA-G6-A8L7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-5P-A9JU         TCGA-A4-A5Y1         TCGA-B1-A47O 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B1-A657         TCGA-BQ-5888         TCGA-BQ-5892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-7056         TCGA-IA-A83W         TCGA-Y8-A8RZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8326         TCGA-KL-8327         TCGA-KL-8329 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8330         TCGA-KL-8331         TCGA-KL-8332 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8333         TCGA-KL-8334         TCGA-KL-8335 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8336         TCGA-KL-8337         TCGA-KL-8338 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8340         TCGA-KL-8341         TCGA-KL-8342 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8343         TCGA-KL-8344         TCGA-KL-8345 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KL-8346         TCGA-KM-8438         TCGA-KM-8443 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8418         TCGA-KN-8419         TCGA-KN-8421 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8422         TCGA-KN-8423         TCGA-KN-8424 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8425         TCGA-KN-8427         TCGA-KN-8428 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KN-8429         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-A3-3308 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3313         TCGA-A3-3317         TCGA-A3-3331 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3335         TCGA-A3-3347         TCGA-A3-3349 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3351         TCGA-A3-3352         TCGA-A3-3357 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3362         TCGA-A3-3363         TCGA-A3-3367 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3370         TCGA-A3-3373         TCGA-A3-3374 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3376         TCGA-A3-3378         TCGA-A3-3380 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-3385         TCGA-A3-3387         TCGA-AK-3426 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3427         TCGA-AK-3428         TCGA-AK-3429 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3430         TCGA-AK-3433         TCGA-AK-3436 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3443         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-B0-5092         TCGA-B0-5094 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5095         TCGA-B0-5096         TCGA-B0-5097 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5104         TCGA-B0-5106         TCGA-B0-5107 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5108         TCGA-B0-5109         TCGA-B0-5110 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5113         TCGA-B0-5115         TCGA-B0-5116 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5119         TCGA-B0-5120         TCGA-B0-5121 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5399         TCGA-B0-5400         TCGA-B0-5692 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5696         TCGA-B0-5697         TCGA-B0-5699 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5701         TCGA-B0-5702         TCGA-B0-5703 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5705         TCGA-B0-5706         TCGA-B0-5710 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B0-5712         TCGA-B0-5713         TCGA-B2-5633 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B2-5641         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-B8-4143         TCGA-B8-4148 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-4151         TCGA-B8-4154         TCGA-B8-4619 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B8-4620         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-BP-4159         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-4329 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4330         TCGA-BP-4332         TCGA-BP-4334 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4335         TCGA-BP-4337         TCGA-BP-4338 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4340         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-4354 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4756         TCGA-BP-4761         TCGA-BP-4768 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4770         TCGA-BP-4771         TCGA-BP-4787 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-4797         TCGA-BP-4798         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-4989         TCGA-BP-5007 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5010         TCGA-BP-5169         TCGA-BP-5182 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BP-5186         TCGA-BP-5198         TCGA-CJ-4638 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4639         TCGA-CJ-4640         TCGA-CJ-4643 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4644         TCGA-CJ-4868         TCGA-CJ-4869 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4872         TCGA-CJ-4873         TCGA-CJ-4874 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4876         TCGA-CJ-4890         TCGA-CJ-4892 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-4900         TCGA-CJ-4918         TCGA-CJ-5678 
"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-4857         TCGA-CZ-4859 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4863         TCGA-CZ-4864         TCGA-CZ-5451 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5452         TCGA-CZ-5454         TCGA-CZ-5456 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5467         TCGA-CZ-5469         TCGA-CZ-5470 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5984         TCGA-CZ-5985         TCGA-CZ-5986 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5988         TCGA-CZ-5989         TCGA-DV-A4VX 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G6-A5PC         TCGA-2Z-A9J1         TCGA-2Z-A9JO 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-5P-A9K9         TCGA-A4-7583         TCGA-A4-7585 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-7915         TCGA-A4-A57E         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-A655 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-B1-A656         TCGA-B9-7268         TCGA-BQ-5877 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-5878         TCGA-BQ-5879         TCGA-BQ-5880 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-5882         TCGA-BQ-5885         TCGA-BQ-5887 
"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-5893         TCGA-BQ-5894         TCGA-BQ-7045 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-BQ-7048         TCGA-BQ-7050         TCGA-BQ-7051 
"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-J7-6720         TCGA-J7-8537         TCGA-J7-A8I2 
"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-P4-AAVK         TCGA-P4-AAVL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A71R         TCGA-SX-A7SM         TCGA-SX-A7SP 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UN-AAZ9         TCGA-UZ-A9PM 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PQ         TCGA-UZ-A9PX         TCGA-Y8-A897 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
D65V6, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     3   0
  12Q LOSS WILD-TYPE 543  89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      3    0
  12Q LOSS WILD-TYPE  543   89
   clus
vv  12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  0                3                543
  1                0                 89
[1] 2 2
[1] FALSE
D65V7, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1   3
  12Q LOSS WILD-TYPE 291 587
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    3
  12Q LOSS WILD-TYPE  291  587
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                1                291
  MALE                  3                587
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1   0
  12Q LOSS WILD-TYPE 407   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1    0
  12Q LOSS WILD-TYPE  407    3
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                407
  YES                0                  3
[1] 2 2
[1] FALSE
D65V9, continuous
[1] "Remove cluster labels:" "12Q LOSS MUTATED"      
clus
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 1                142 
        TCGA-KM-8439         TCGA-KM-8441         TCGA-KM-8442 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-CZ-4854         TCGA-CZ-4856 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-DV-5565         TCGA-DV-5566 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4W0         TCGA-G6-A8L7 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8440         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-KN-8429         TCGA-KN-8434         TCGA-KO-8413 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3428 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-AK-3430         TCGA-B0-4838         TCGA-B2-5639 
"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-B8-4622         TCGA-B8-5158 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CZ-4858         TCGA-CZ-4860 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-5456         TCGA-CZ-5458 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-DV-A4VX         TCGA-DV-A4VZ         TCGA-EU-5904 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L8         TCGA-T7-A92I 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-4A-A93W         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-A4-8098 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-A4-A48D         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-7963         TCGA-EV-5901 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         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-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU         TCGA-UZ-A9PL 
"12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" "12Q LOSS WILD-TYPE" 
        TCGA-V9-A7HT 
"12Q LOSS WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  12Q LOSS MUTATED                    1                                 3
  12Q LOSS WILD-TYPE                 65                               525
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  12Q LOSS MUTATED                                       0
  12Q LOSS WILD-TYPE                                   288
D65V10, multiclass
                                       clus
vv                                      12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   1                 65
  KIDNEY CLEAR CELL RENAL CARCINOMA                    3                525
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                0                288
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
D65V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  12Q LOSS MUTATED                                  0     0
  12Q LOSS WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED                           0     4
  12Q LOSS WILD-TYPE                       121   715
D65V13, multiclass
                                  clus
vv                                 12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       0                121
  WHITE                                           4                715
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V14, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     0   2
  12Q LOSS WILD-TYPE  42 620
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      0    2
  12Q LOSS WILD-TYPE   42  620
                        clus
vv                       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO                2                620
[1] 2 2
[1] FALSE

Clustering(66) Variable = 13Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED    85  50
  13Q LOSS WILD-TYPE 563 178
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
               135                741 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                50                178 
$`13Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
      102.81        28.11        47.24        19.73        43.96        52.21 
TCGA-BP-5191 TCGA-CZ-4854 TCGA-DV-5568 TCGA-G6-A8L7 TCGA-AL-A5DJ TCGA-B3-A6W5 
       31.79        46.16        12.16        70.13        49.25        10.16 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       38.07       153.73       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8476 TCGA-KN-8418 
       66.54        24.79       151.96        44.91       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
       87.91        25.48        65.19       104.52         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 
       87.12        19.33         2.50        59.08       115.00       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 
      105.60        90.48        92.55        37.15         4.50        52.93 
TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3426 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3445 
       74.76        43.20        29.10       112.08        94.19        78.64 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4696 
       12.13        40.70         3.32         1.41         4.57        28.47 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
        1.38         3.62         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 
       38.63        52.87        85.78         5.10         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-CJ-4868 TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 
       21.24        66.21        47.67        25.71        22.32        53.42 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CW-6097 TCGA-CZ-4860 TCGA-CZ-4863 TCGA-CZ-4866 
       66.31        83.90        18.77         6.77        63.39       107.41 
TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 
       18.44        90.54        84.30         1.94        31.10        67.96 
TCGA-2Z-A9JI TCGA-5P-A9K8 TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-3926 TCGA-BQ-5875 
       51.52        43.04        19.63         0.23        29.03        86.76 
TCGA-BQ-5879 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6793 
       22.92         2.76        10.68        13.08         4.01        11.05 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 
       25.84        23.08        16.90         3.68         2.04        10.55 
TCGA-P4-A5E8 TCGA-Q2-A5QZ TCGA-UN-AAZ9 
       42.94        14.07        18.02 

$`13Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KO-8411 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 
       23.28        28.80       130.13        47.21        38.47        34.29 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       31.07        42.97        82.32       109.91        58.49        28.73 
TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       22.45        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5199 
       35.90        48.10        62.86        49.15        27.02        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 
       53.26       118.85        75.58       103.43         0.59       107.54 
TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 
        5.46        43.69        45.96        65.88        11.67        37.15 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-MM-A84U TCGA-2Z-A9J9 
       66.28        56.84        23.90        81.21        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 
       12.26        67.17        61.05        21.37         0.89        12.99 
TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5155 TCGA-B9-A44B 
       76.64        21.67        27.68        21.07        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8325 
       86.37        21.60        15.91        15.62         6.74        23.84 
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 
      109.22        98.33        73.91        71.41        28.80        54.74 
TCGA-KL-8346 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
       62.37        49.97        51.06        31.33        23.47        25.91 
TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8410 TCGA-KO-8413 
        3.55        11.21        42.35       100.87       103.10        99.88 
TCGA-KO-8415 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       96.62        12.66        11.90        36.82         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3349 TCGA-A3-3351 
       38.99        37.38        48.82        62.01        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        51.25        10.49        28.70        74.63 
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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 
      109.41        15.78        73.68        68.61       109.51        46.78 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       48.36        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       82.45        72.89         1.41         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4821 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-B0-4828 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
        7.30        25.32         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       19.30        66.05        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        1.25         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 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        40.04        23.74         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 
       15.62         0.07        18.48        52.24        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        31.89        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 
        5.98        41.75        71.80        48.07        61.68         5.33 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 
       61.97        13.51        56.91        68.38        60.95        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.53        36.39        10.98        36.95         6.71        47.97 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 
       87.45        71.41        63.62        58.68        60.30         6.74 
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         6.94        47.11 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       14.93        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 
       46.45        16.47        30.64        18.51        38.70        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
       24.62        33.47        19.82        34.95         0.95       115.00 
TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        73.22        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        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-4882 
       74.27        75.06       116.84        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       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       56.35        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
      131.08        72.00       129.40       133.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 
       18.15       122.83        62.10        73.35        67.00        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4864 
       25.45        47.08        69.21        58.75        14.66        93.04 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5456 TCGA-CZ-5458 
       63.42        58.82        79.53        23.74        79.63        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 
       22.52         2.40        12.69        80.19        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN 
       91.73        56.81        54.64        38.99        30.71        24.33 
TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y 
       31.20        29.36         5.29         0.13        12.82        11.57 
TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 
      106.55        49.58        90.21        22.26        78.64        15.48 
TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       71.80        62.93        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        18.21         0.10        35.18        19.13         7.82 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 
        2.20        41.13        37.51        36.49        20.25        16.77 
TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       20.32        33.83        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-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-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        0.95         7.92       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-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 
       90.90        39.25        71.44        25.15        20.52        25.25 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 
       12.43        12.89        11.21        16.31        81.93        58.19 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 
       19.99        85.78        88.24        96.69        22.26        21.34 
TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.36        12.76        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EA TCGA-P4-A5EB 
       31.13        15.48        99.78        87.09         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ 
       16.31        41.62        26.47        53.10        43.76        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.23               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            153.73             194.79 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             38.63              35.18 
[1] "0.2 - 153.7 (38.6)" "0.1 - 194.8 (35.2)"
[1] "hr=" "1.4"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  13Q LOSS MUTATED        43       21        44       28
  13Q LOSS WILD-TYPE     411       82       146       76
D66V3, multiclass
           clus
vv          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                 43                411
  STAGE II                21                 82
  STAGE III               44                146
  STAGE IV                28                 76
[1] 4 2
[1] TRUE
[1] "dimension of 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  60   9
  13Q LOSS WILD-TYPE 435 104 198   6
D66V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1               45                435
  T2               23                104
  T3               60                198
  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 260  30   2
D66V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0               63                260
  N1               14                 30
  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 466  70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     80   19
  13Q LOSS WILD-TYPE  466   70
   clus
vv  13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  0               80                466
  1               19                 70
[1] 2 2
[1] FALSE
D66V7, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    58  79
  13Q LOSS WILD-TYPE 234 511
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     58   79
  13Q LOSS WILD-TYPE  234  511
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               58                234
  MALE                 79                511
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED    72   0
  13Q LOSS WILD-TYPE 336   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     72    0
  13Q LOSS WILD-TYPE  336    3
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                72                336
  YES                0                  3
[1] 2 2
[1] FALSE
D66V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  13Q LOSS MUTATED                   43                                71
  13Q LOSS WILD-TYPE                 23                               457
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  13Q LOSS MUTATED                                      23
  13Q LOSS WILD-TYPE                                   265
D66V10, multiclass
                                       clus
vv                                      13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  43                 23
  KIDNEY CLEAR CELL RENAL CARCINOMA                   71                457
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               23                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"
D66V11, continuous
D66V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  13Q LOSS MUTATED                                  0     4
  13Q LOSS WILD-TYPE                                2    12
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED                          12   117
  13Q LOSS WILD-TYPE                       109   602
D66V13, multiclass
                                  clus
vv                                 13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           4                 12
  BLACK OR AFRICAN AMERICAN                      12                109
  WHITE                                         117                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"
D66V14, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     4  87
  13Q LOSS WILD-TYPE  38 535
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4   87
  13Q LOSS WILD-TYPE   38  535
                        clus
vv                       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               87                535
[1] 2 2
[1] FALSE

Clustering(67) Variable = 14Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  14Q LOSS MUTATED   158 106
  14Q LOSS WILD-TYPE 490 122
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               264                612 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
               106                122 
$`14Q LOSS MUTATED`
TCGA-A3-3336 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
       34.29        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5694 TCGA-B0-5698 TCGA-B2-5635 TCGA-B8-5162 TCGA-BP-4164 
       52.21        15.78       119.38        24.82         1.18        32.61 
TCGA-BP-4331 TCGA-BP-4353 TCGA-BP-4965 TCGA-BP-4986 TCGA-BP-5009 TCGA-BP-5178 
       80.68        12.33        61.51        25.81        35.90        62.86 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       27.02        31.79        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CZ-4854 TCGA-DV-5573 
       27.65        53.26       118.85        75.58        46.16        37.15 
TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-BQ-5888 TCGA-PJ-A5Z8 TCGA-KL-8344 
       23.01        12.99        49.25        13.25        19.73        28.80 
TCGA-KN-8427 TCGA-A3-3306 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 
        0.99        36.82        39.16        49.08        49.02        37.15 
TCGA-A3-3320 TCGA-A3-3324 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3351 
       49.58        38.99        62.01         4.50        52.93        29.92 
TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-A3-A6NI TCGA-AK-3426 
       88.37        20.71        18.87        20.28        33.47        29.10 
TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3451 TCGA-AK-3458 
      117.80       109.41        15.78       109.51        94.29        38.40 
TCGA-B0-4691 TCGA-B0-4694 TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4814 TCGA-B0-4817 
        4.57         3.48         5.98         6.64         5.52        33.50 
TCGA-B0-4819 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
        6.02        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5081 
       26.07        29.03        36.85        70.52        20.94        11.90 
TCGA-B0-5084 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5106 
        7.30        15.09        10.95         2.24        21.86        52.54 
TCGA-B0-5107 TCGA-B0-5113 TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5701 
       30.48        38.63        56.98       129.67        86.47        80.91 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-4098 TCGA-B2-4102 TCGA-B2-5633 
       79.89       131.15        89.49         1.68        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
       32.98        21.57         5.10         4.64         5.46         0.36 
TCGA-B8-4143 TCGA-B8-4619 TCGA-B8-5158 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 
       23.31        17.19        40.04         0.85        48.53         0.53 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4167 
       14.30        27.29         1.74         4.93        93.34        89.36 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       62.24        61.78        64.27        62.86        49.08        44.94 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4768 TCGA-BP-4771 
       11.31        33.99         5.98        41.75        13.15         5.33 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4803 
       56.91        68.38        15.78        36.39        10.98         6.71 
TCGA-BP-4959 TCGA-BP-4962 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 
       87.45        58.68        14.24        48.89        45.50        14.93 
TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 
       36.07        46.45         3.88        16.47        18.51        37.02 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 
        6.35        79.30         2.04        74.20        30.64        74.40 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4637 
       42.44        37.22        33.24        33.47        19.82        73.22 
TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
       14.17       114.41        54.61        11.05        21.24        83.97 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 
       79.66        74.27        75.06       116.84        64.27        66.21 
TCGA-CJ-4884 TCGA-CJ-4888 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4907 
       57.83        51.52        24.66       109.84        51.29        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4920 TCGA-CJ-4923 
       50.33        54.48        38.56        45.14         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-6033 TCGA-CW-5580 
       22.32        25.25       122.83        67.00         7.36        64.57 
TCGA-CW-5584 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6097 
        5.39        73.18        66.31         1.35        83.90        18.77 
TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       69.21         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5452 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       58.82        18.44        79.63        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
       84.30         1.94        31.10        12.69        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-G6-A5PC TCGA-MM-A563 TCGA-2Z-A9JG 
       14.63        62.63        53.46         7.96        19.43        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-5P-A9K3 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-A4-7286 
       51.52        38.99        15.48        43.04        19.36        18.21 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-8098 TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-7173 
       19.63         0.10        29.46         9.63        62.66        67.73 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 
       37.51        16.77        29.03        20.61        17.23        19.27 
TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5894 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ 
       30.28        10.82         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        71.44        20.52        25.84 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y 
       23.08        16.90        27.65        73.25        16.80         2.04 
TCGA-MH-A854 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-WN-A9G9 
       17.62         6.61        14.07        18.02        37.35        26.01 

$`14Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       47.21        38.47        31.07        42.97        82.32       109.91 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5812 TCGA-B8-4621 
       18.51       112.80       133.94        70.68       126.05        25.91 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4342 
        8.42        15.42       111.02        94.72         3.58        74.17 
TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       54.77        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 
       37.25         6.94        53.65        27.22         5.82        45.07 
TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5168 TCGA-BP-5181 TCGA-BP-5199 TCGA-CJ-4904 
       41.62        27.62        48.10        49.15        44.55       108.56 
TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
      103.43         0.59       107.54         5.46        43.69        45.96 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       65.88        12.16        11.67        66.28        56.84        23.90 
TCGA-DV-A4W0 TCGA-G6-A8L7 TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       81.21        70.13        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 
       21.37         0.89        76.64        21.67        27.68        21.07 
TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5892 
       10.16        21.86        11.87        19.23        26.04        11.97 
TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 
       96.92        44.84        26.27        20.12        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       67.17        16.34        12.13        29.26        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       71.41        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 
       87.12        19.33         2.50        11.21        59.08       115.00 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 
       42.35       100.87       105.47        10.68       100.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 
       92.71        16.67       104.55       103.10        99.88       105.60 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 
       96.62        90.48        92.55        12.66        11.90         0.53 
TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3349 
       24.16        48.59        36.36        37.38        48.82        45.53 
TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       18.44        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 
       24.16        53.29        43.20        55.76        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-3428 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 
       10.62       122.56        73.68       112.08        68.61        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 
       46.78        48.36        78.64        40.01        83.21        37.58 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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        57.70         3.25        58.45 
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        10.52        10.29        65.29        39.45 
TCGA-B0-4849 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5085 TCGA-B0-5095 TCGA-B0-5098 
        2.27        43.30        11.24        25.32         8.05        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5108 TCGA-B0-5109 
       15.95        62.89        90.87        90.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5696 TCGA-B0-5699 
       48.82        46.39        42.41       111.52        85.78       126.28 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 
       71.41        73.84       149.16       105.37       130.65        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 
       32.61        35.90        31.96        21.30        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
        5.75         1.25         0.53         0.23        16.80        49.97 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 
       42.71        25.05        45.37        25.55        50.14        23.74 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 
       27.02        24.23        50.14        16.60         6.38        34.39 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
       29.88        17.06        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 
       90.28       101.06        99.85         0.43        23.05        77.03 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        31.89        31.33        12.30        72.59        77.98 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4776 
       71.80        48.07        61.68        10.82        61.97        13.51 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4960 
       60.95        48.95        36.53        36.95        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
       63.62        60.30        61.22         6.74        57.40        58.98 
TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 
       49.38         6.94        47.11        33.34        31.30        36.95 
TCGA-BP-4991 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 
       46.45        43.00        30.64        38.70        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 
       28.87        52.27         9.63        38.30        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 
       13.35        23.47        13.41        24.62        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4872 
      115.00        46.55       106.16        58.95        49.25        47.18 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 
       71.87        61.91       113.46        64.18        30.64        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
      115.69        50.01        39.45        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4918 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 
       49.97        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       119.64        92.02        81.83        85.78 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 
       78.18        74.66       105.93        25.45        47.08        58.75 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       63.42        79.53        23.74        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5982 TCGA-CZ-5986 
       94.45        69.96        22.52         2.40        80.19        12.26 
TCGA-CZ-5988 TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       22.78        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I 
       10.29        35.87         2.01        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
        4.57        91.73        56.81        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        71.80        62.93 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7585 TCGA-A4-7732 
       12.99        12.39        27.09        67.43        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 
        7.82         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-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-5398 
       12.46        70.19        49.32        66.71         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       36.49        20.25        20.32        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       43.99        22.06         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
       21.63        40.83        26.04        25.35         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
       51.19        74.60        34.19        19.00        24.89         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
        1.18         0.43        51.78        90.90        39.25        25.15 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       25.25        17.98        80.65       194.79        12.92         3.68 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X 
       58.19        26.01        11.84        56.75        25.22        19.99 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A856 
       34.29        27.78        30.38        27.65        20.25        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED 
       15.48        99.78        87.09        42.94        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-AB4C 
       47.47        65.13       110.73        51.35        31.73        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.10               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            133.71             194.79 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            31.725             37.250 
[1] "0.1 - 133.7 (31.7)" "0.1 - 194.8 (37.2)"
[1] "hr=" "2.2"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  14Q LOSS MUTATED        97       29        77       54
  14Q LOSS WILD-TYPE     357       74       113       50
D67V3, multiclass
           clus
vv          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                 97                357
  STAGE II                29                 74
  STAGE III               77                113
  STAGE IV                54                 50
[1] 4 2
[1] TRUE
[1] "dimension of 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   105  39 117   4
  14Q LOSS WILD-TYPE 375  88 141  11
D67V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1              105                375
  T2               39                 88
  T3              117                141
  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   102  23   4
  14Q LOSS WILD-TYPE 221  21   2
D67V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0              102                221
  N1               23                 21
  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"
D67V6, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED   175  49
  14Q LOSS WILD-TYPE 371  40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED    175   49
  14Q LOSS WILD-TYPE  371   40
   clus
vv  14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  0              175                371
  1               49                 40
[1] 2 2
[1] FALSE
D67V7, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    86 179
  14Q LOSS WILD-TYPE 206 411
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     86  179
  14Q LOSS WILD-TYPE  206  411
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               86                206
  MALE                179                411
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    77   2
  14Q LOSS WILD-TYPE 331   1
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     77    2
  14Q LOSS WILD-TYPE  331    1
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                77                331
  YES                2                  1
[1] 2 2
[1] FALSE
D67V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  14Q LOSS MUTATED                    2                               216
  14Q LOSS WILD-TYPE                 64                               312
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  14Q LOSS MUTATED                                      47
  14Q LOSS WILD-TYPE                                   241
D67V10, multiclass
                                       clus
vv                                      14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                  216                312
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               47                241
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
D67V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  14Q LOSS MUTATED                                  0     3
  14Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED                          24   231
  14Q LOSS WILD-TYPE                        97   488
D67V13, multiclass
                                  clus
vv                                 14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 13
  BLACK OR AFRICAN AMERICAN                      24                 97
  WHITE                                         231                488
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V14, binary
                    cls
clus                   0   1
  14Q LOSS MUTATED    13 187
  14Q LOSS WILD-TYPE  29 435
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     13  187
  14Q LOSS WILD-TYPE   29  435
                        clus
vv                       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   13                 29
  NOT HISPANIC OR LATINO              187                435
[1] 2 2
[1] FALSE

Clustering(68) Variable = 15Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  15Q LOSS MUTATED    40  28
  15Q LOSS WILD-TYPE 608 200
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                68                808 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                28                200 
$`15Q LOSS MUTATED`
TCGA-B0-4712 TCGA-BP-4164 TCGA-BP-4775 TCGA-BP-5178 TCGA-A4-A5Y1 TCGA-PJ-A5Z8 
       43.96        32.61        60.59        62.86        12.99        19.73 
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-B0-4821 TCGA-B0-5080 TCGA-B0-5084 TCGA-B0-5095 TCGA-B0-5116 TCGA-B4-5832 
       40.44        11.24         7.30         8.05        41.88         5.10 
TCGA-B8-4620 TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4768 
       25.55         6.38        89.36        62.86        11.31        13.15 
TCGA-BP-4797 TCGA-BP-4985 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5200 TCGA-CJ-4901 
       36.39        31.30         6.35        30.64        34.95        47.67 
TCGA-CJ-4907 TCGA-CJ-5677 TCGA-CJ-6028 TCGA-CZ-4857 TCGA-CZ-4860 TCGA-CZ-5457 
       49.28        25.71        53.42        47.08         6.77        90.54 
TCGA-CZ-5461 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-G6-A8L8 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       10.85        31.10        67.96        35.87        54.64        51.52 
TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-7583 TCGA-B1-5398 
       12.82        49.58        19.36        18.21         0.10        41.13 
TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5889 TCGA-BQ-5894 
       29.03        17.23        22.92        21.63        10.82         2.76 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A8LC 
       10.68        13.08         4.01        71.44        25.84        23.08 
TCGA-GL-7966 TCGA-HE-7130 TCGA-HE-A5NK TCGA-P4-A5EA TCGA-UN-AAZ9 TCGA-UZ-A9PP 
        3.68        58.19        73.25         6.61        18.02        98.96 
TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.64        13.28 

$`15Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4815 
      109.91        58.49        28.73        22.45        19.73        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 
      111.02        94.72         3.58        80.68        74.17        54.77 
TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       12.33        77.62        44.15        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5181 
       45.07        41.62        27.62        35.90        48.10        49.15 
TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 
       27.02        31.79        44.55        31.27        63.25       105.37 
TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 
       26.93        27.65       108.56        53.26       118.85        75.58 
TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 
      103.43        46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 
       56.84        23.90        81.21        70.13        23.01        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       16.34        12.13        29.26        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 
       98.96        84.89        98.33        96.95        92.55        30.25 
TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 
       44.84        86.56        66.54        24.79        73.91        71.41 
TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-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       105.47        10.68       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 
       16.67       104.55       103.10        99.88       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
       90.48        92.55        12.66        11.90        36.82         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-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A3-3383 TCGA-A3-3385 
       43.20        55.76        20.71        18.64        28.31        65.52 
TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 
       19.00         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 
       57.70         6.64         3.25        58.45        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59         5.52        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4834 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        10.52        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 
       11.90        25.32        15.09        10.95         2.24        21.86 
TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       52.08        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        58.59        19.30        66.05        38.63        52.73 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
       21.57        16.67        12.00         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-B8-4622 
       49.97        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       40.04        23.74        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 
       49.08        44.94        12.23        31.89        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 
       38.70        37.02        37.48        35.21        28.87        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 
        2.04        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-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5202 
       23.47        13.41        24.62        33.47        19.82         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
      115.00        46.55        73.22        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45       109.84        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-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        67.00        62.66       119.64         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-6097 
       78.18        74.66         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       25.45        69.21        58.75        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5462 TCGA-CZ-5463 
       79.63        91.69        55.33        94.45        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5470 
       69.96        84.30        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC 
        7.96        10.29         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        91.73        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y 
       24.33        31.20        29.36         5.29         0.13        11.57 
TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
      106.55        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
       19.63        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 
       20.61         0.46         1.15        43.99        22.06         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-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       63.72        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 
       25.35         7.66         0.95         7.92       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        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        90.90        11.05        39.25        25.15 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       20.52        25.25        17.98        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
       12.92        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
       16.31        81.93        26.01        11.84        56.75        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       16.80        19.99         2.04        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.05        25.28         6.02 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.10               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             98.96             194.79 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            24.315             36.950 
[1] "0.1 - 99.0 (24.3)"  "0.1 - 194.8 (37.0)"
[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     434       99       167       87
D68V3, multiclass
           clus
vv          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                 20                434
  STAGE II                 4                 99
  STAGE III               23                167
  STAGE IV                17                 87
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q LOSS MUTATED    23   5  36   4
  15Q LOSS WILD-TYPE 457 122 222  11
D68V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1               23                457
  T2                5                122
  T3               36                222
  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
  15Q LOSS MUTATED    22   9   2
  15Q LOSS WILD-TYPE 301  35   4
D68V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               22                301
  N1                9                 35
  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"
D68V6, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    34  13
  15Q LOSS WILD-TYPE 512  76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     34   13
  15Q LOSS WILD-TYPE  512   76
   clus
vv  15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  0               34                512
  1               13                 76
[1] 2 2
[1] FALSE
D68V7, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    20  48
  15Q LOSS WILD-TYPE 272 542
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     20   48
  15Q LOSS WILD-TYPE  272  542
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               20                272
  MALE                 48                542
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED    29   0
  15Q LOSS WILD-TYPE 379   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     29    0
  15Q LOSS WILD-TYPE  379    3
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                29                379
  YES                0                  3
[1] 2 2
[1] FALSE
D68V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  15Q LOSS MUTATED                    2                                36
  15Q LOSS WILD-TYPE                 64                               492
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  15Q LOSS MUTATED                                      30
  15Q LOSS WILD-TYPE                                   258
D68V10, multiclass
                                       clus
vv                                      15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   2                 64
  KIDNEY CLEAR CELL RENAL CARCINOMA                   36                492
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               30                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"
D68V11, continuous
D68V12, continuous
[1] "Remove cluster labels:" "15Q LOSS MUTATED"      
clus
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                 2                 72 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-B8-5550 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J3 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117         TCGA-B9-A69E 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6793 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-6795         TCGA-G7-7501         TCGA-G7-A8LB 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-GL-7773 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71S 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A71U         TCGA-SX-A7SL         TCGA-SX-A7SM 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-SX-A7SR         TCGA-SX-A7SS         TCGA-UZ-A9PM 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" "15Q LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A8RY 
"15Q LOSS WILD-TYPE" "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    14
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED                           5    57
  15Q LOSS WILD-TYPE                       116   662
D68V13, multiclass
                                  clus
vv                                 15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           2                 14
  BLACK OR AFRICAN AMERICAN                       5                116
  WHITE                                          57                662
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V14, binary
                    cls
clus                   0   1
  15Q LOSS MUTATED     1  47
  15Q LOSS WILD-TYPE  41 575
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      1   47
  15Q LOSS WILD-TYPE   41  575
                        clus
vv                       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               47                575
[1] 2 2
[1] FALSE

Clustering(69) Variable = 16P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     7  11
  16P LOSS WILD-TYPE 641 217
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                18                858 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                11                217 
$`16P LOSS MUTATED`
TCGA-KL-8339 TCGA-KL-8336 TCGA-KN-8427 TCGA-KO-8408 TCGA-A3-3316 TCGA-A3-A6NN 
       28.11        30.25         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 TCGA-HE-7130 
       31.30        80.19        19.63        21.63        11.05        58.19 

$`16P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M 
       21.37         0.89        12.99        76.64        49.25        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 
       21.60        15.91        15.62         6.74        38.07       153.73 
TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       23.84       109.22       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 
       62.37       151.96        44.91        49.97       123.12        51.06 
TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 
       31.33       129.37        23.47        87.91        25.48        25.91 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-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 
      105.47        10.68       100.47       103.40        92.71       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OV TCGA-A3-A8OW 
       33.47        15.39        22.65         0.10        11.18        10.62 
TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 
       82.45        72.89        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-B0-4710 
        3.62        65.10         7.82         5.98         2.14        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 
        5.52        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-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90         7.30        25.32        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        2.24        21.86        52.08        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       38.63        52.73        41.88        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.53        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       69.96        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       54.64        51.52        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 
       49.58        90.21        22.26        78.64        15.48        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE 
       62.93        43.04        19.36        12.99        12.39        27.09 
TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 
       67.43        18.21         0.10        35.18        19.13         7.82 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
        0.23        16.64        30.48        29.46        25.64        23.97 
TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 
       12.46         9.63        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
       22.92        43.20        47.80        40.83        26.04        30.28 
TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 
       25.35        10.82         7.66         0.95         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       10.68        13.08         2.40         1.18         0.43         4.01 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        90.90        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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 
            28.290             36.425 
[1] "0.1 - 80.2 (28.3)"  "0.1 - 194.8 (36.4)"
[1] "hr=" "3.7"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16P LOSS MUTATED         4        2         6        6
  16P LOSS WILD-TYPE     450      101       184       98
D69V3, multiclass
           clus
vv          16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                  4                450
  STAGE II                 2                101
  STAGE III                6                184
  STAGE IV                 6                 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
  16P LOSS MUTATED     4   2   9   3
  16P LOSS WILD-TYPE 476 125 249  12
D69V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                4                476
  T2                2                125
  T3                9                249
  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 317  40   4
D69V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                6                317
  N1                4                 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"
D69V6, binary
                    cls
clus                   0   1
  16P LOSS MUTATED    11   2
  16P LOSS WILD-TYPE 535  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     11    2
  16P LOSS WILD-TYPE  535   87
   clus
vv  16P LOSS MUTATED 16P LOSS WILD-TYPE
  0               11                535
  1                2                 87
[1] 2 2
[1] FALSE
D69V7, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7  11
  16P LOSS WILD-TYPE 285 579
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7   11
  16P LOSS WILD-TYPE  285  579
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                7                285
  MALE                 11                579
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   0
  16P LOSS WILD-TYPE 401   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    0
  16P LOSS WILD-TYPE  401    3
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 7                401
  YES                0                  3
[1] 2 2
[1] FALSE
D69V9, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                141 
        TCGA-KM-8439         TCGA-KM-8441         TCGA-KM-8442 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-CZ-4854         TCGA-CZ-4856 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-DV-5565         TCGA-DV-5566 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4W0         TCGA-G6-A8L7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8440         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-KN-8429         TCGA-KN-8434         TCGA-KO-8413 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-3Z-A93Z         TCGA-A3-A6NJ         TCGA-A3-A6NL 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A3-A8CQ         TCGA-AK-3426         TCGA-AK-3428 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AK-3430         TCGA-B0-4838         TCGA-B2-5639 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5377         TCGA-B4-5378         TCGA-B4-5832 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5834         TCGA-B4-5835         TCGA-B4-5836 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B4-5838         TCGA-B4-5843         TCGA-B4-5844 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-4143         TCGA-B8-4622         TCGA-B8-5158 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CJ-6028         TCGA-CZ-4858         TCGA-CZ-4860 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-4861         TCGA-CZ-5456         TCGA-CZ-5457 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-CZ-5458         TCGA-CZ-5465         TCGA-CZ-5469 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DV-A4VX         TCGA-DV-A4VZ         TCGA-EU-5904 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L8         TCGA-T7-A92I 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93W         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-A4-8098 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A48D         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-7963         TCGA-EV-5901 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6795         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-A7SP 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SQ         TCGA-SX-A7SR         TCGA-SX-A7SS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-SX-A7SU         TCGA-UZ-A9PL         TCGA-V9-A7HT 
"16P LOSS WILD-TYPE" "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                               518
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16P LOSS MUTATED                                       4
  16P LOSS WILD-TYPE                                   284
D69V10, multiclass
                                       clus
vv                                      16P LOSS MUTATED 16P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                   10                518
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                4                284
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                104 
        TCGA-B8-4621         TCGA-DV-A4W0         TCGA-G6-A8L7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-KL-8324         TCGA-KL-8330 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KL-8335         TCGA-KL-8341         TCGA-KL-8345 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KM-8639         TCGA-KN-8428         TCGA-KN-8433 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416         TCGA-A3-A8CQ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-4146 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-5550 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-G6-A5PC 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J2 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"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-4A-A93W 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9K3         TCGA-5P-A9KE 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-A48D         TCGA-A4-A57E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3466         TCGA-AL-3472 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6795         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-HE-A5NJ         TCGA-HE-A5NK         TCGA-IA-A40U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-IA-A83S         TCGA-IA-A83V         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-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-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 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
D69V12, continuous
[1] "Remove cluster labels:" "16P LOSS MUTATED"      
clus
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 2                 72 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5550         TCGA-MM-A563 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-T7-A92I         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117         TCGA-B9-A69E 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6795 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-IA-A40U         TCGA-MH-A854 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-MH-A856         TCGA-P4-A5E6         TCGA-P4-AAVK 
"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-A9PS 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" "16P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"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    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED                           2    14
  16P LOSS WILD-TYPE                       119   705
D69V13, multiclass
                                  clus
vv                                 16P LOSS MUTATED 16P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       2                119
  WHITE                                          14                705
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V14, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   8
  16P LOSS WILD-TYPE  42 614
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    8
  16P LOSS WILD-TYPE   42  614
                        clus
vv                       16P LOSS MUTATED 16P LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO                8                614
[1] 2 2
[1] FALSE

Clustering(70) Variable = 16Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    12  16
  16Q LOSS WILD-TYPE 636 212
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                28                848 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                16                212 
$`16Q LOSS MUTATED`
TCGA-KL-8339 TCGA-A4-A5Y1 TCGA-KL-8336 TCGA-KN-8427 TCGA-KN-8428 TCGA-KO-8408 
       28.11        12.99        30.25         0.99        52.27        16.67 
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-A6NN TCGA-B0-4822 TCGA-B0-4836 TCGA-B0-4837 
       36.82        49.08         0.10        36.53        40.70        45.30 
TCGA-B0-5097 TCGA-B0-5402 TCGA-B8-5551 TCGA-BP-4354 TCGA-BP-4770 TCGA-BP-4797 
       21.86        42.41         0.53        33.99        10.82        36.39 
TCGA-BP-4985 TCGA-CZ-5982 TCGA-G6-A8L8 TCGA-MM-A564 TCGA-2Z-A9JI TCGA-A4-7287 
       31.30        80.19        35.87        19.96        51.52        19.63 
TCGA-BQ-5882 TCGA-G7-6793 TCGA-G7-A8LD TCGA-HE-7130 
       21.63        11.05        16.90        58.19 

$`16Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 
       58.49        28.73        22.45        19.73        43.96        52.21 
TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 
       18.51       112.80       133.94        15.78        70.68       119.38 
TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K 
      126.05        24.82        25.91         1.18         8.42        15.42 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
      111.02        94.72        32.61         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       11.28        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       24.46        13.78         3.75        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ 
       19.73        17.75        41.33        62.83        86.37        21.60 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       15.91        15.62         6.74        38.07       153.73        23.84 
TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 
      109.22       137.06        90.48       108.62        98.96        84.89 
TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       98.33        96.95        92.55        44.84        86.56        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
      104.52         3.55        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
      100.47       103.40        92.71       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
      105.60        96.62        90.48        92.55        12.66        11.90 
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-A3-3322 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        62.01 
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-A3-3362 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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       28.31        65.52        20.28        33.47        15.39        22.65 
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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        40.44        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4838 TCGA-B0-4839 
       29.10        10.09        78.44        68.71        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 
       43.30        11.24        11.90         7.30        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 
       38.43        48.82        46.39        56.98       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       91.46        32.61        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
        5.75         5.10         1.25         0.53         4.64         5.46 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
        0.36         0.23        23.31        16.80        49.97        42.71 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 
       25.05        45.37        17.19        25.55        50.14        40.04 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        50.14        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
        6.38        48.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 
       31.33        12.30        72.59        77.98         5.98        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 TCGA-BP-4787 TCGA-BP-4789 
       13.51        56.91        68.38        60.95        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.53        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-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-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        6.94        47.11        14.93        36.07        33.34        46.45 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       18.51        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         2.04        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       33.47        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06       116.84        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83       113.46        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 
       63.98       115.69        50.01        24.66        39.45       109.84 
TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
       50.24        56.35        47.67        49.97        51.29        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81       131.08        72.00       129.40       133.71 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
       25.71        18.87        22.32        25.25        18.15       122.83 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 
       62.10        73.35        67.00        53.42        62.66       119.64 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       83.90        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
       69.96        84.30        22.52         2.40         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       12.69        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        18.12         3.91         6.77 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MW-A4EC 
        4.18         7.96        10.29         2.01        19.43        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK 
       56.91         4.57        91.73        56.81        54.64        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7583 
       12.99        12.39        27.09        67.43        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 
       40.83        26.04        30.28        25.35        10.82         7.66 
TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 
        0.95         7.92         2.76       123.62        48.26        93.34 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       61.28        50.40        49.84         7.63         7.04         7.17 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        3.81        40.77        79.86        80.88        51.19        74.60 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
       34.19        19.00        24.89        10.68        13.08         2.40 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
        1.18         0.43         4.01        51.78        90.90        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
       23.08        80.65       194.79        12.92         3.68        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
       26.01        11.84        56.75        73.25        25.22        16.80 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       19.99         2.04        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD 
       21.34        12.36        12.76        10.55        10.09        18.41 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
       29.10        11.41        34.29        27.78        30.38        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
       20.25        17.62        31.13        15.48        99.78        87.09 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       42.94         6.61        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       50.60        78.90        14.07        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS 
      103.63       125.29        37.35        98.96        86.27        71.24 
TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT 
       30.67        47.47        65.13       110.73        51.35        31.73 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY 
       26.01        39.06        18.64        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  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 
            30.775             36.215 
[1] "0.1 - 80.2 (30.8)"  "0.1 - 194.8 (36.2)"
[1] "hr=" "3.2"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  16Q LOSS MUTATED         7        4         9        8
  16Q LOSS WILD-TYPE     447       99       181       96
D70V3, multiclass
           clus
vv          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                  7                447
  STAGE II                 4                 99
  STAGE III                9                181
  STAGE IV                 8                 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
  16Q LOSS MUTATED     8   4  12   4
  16Q LOSS WILD-TYPE 472 123 246  11
D70V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                8                472
  T2                4                123
  T3               12                246
  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 314  38   4
D70V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                9                314
  N1                6                 38
  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 532  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     14    3
  16Q LOSS WILD-TYPE  532   86
   clus
vv  16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  0               14                532
  1                3                 86
[1] 2 2
[1] FALSE
D70V7, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     9  19
  16Q LOSS WILD-TYPE 283 571
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      9   19
  16Q LOSS WILD-TYPE  283  571
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                9                283
  MALE                 19                571
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    14   0
  16Q LOSS WILD-TYPE 394   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     14    0
  16Q LOSS WILD-TYPE  394    3
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                14                394
  YES                0                  3
[1] 2 2
[1] FALSE
D70V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  16Q LOSS MUTATED                    5                                16
  16Q LOSS WILD-TYPE                 61                               512
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  16Q LOSS MUTATED                                       7
  16Q LOSS WILD-TYPE                                   281
D70V10, multiclass
                                       clus
vv                                      16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   5                 61
  KIDNEY CLEAR CELL RENAL CARCINOMA                   16                512
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                7                281
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
D70V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  16Q LOSS MUTATED                                  0     0
  16Q LOSS WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED                           4    22
  16Q LOSS WILD-TYPE                       117   697
D70V13, multiclass
                                  clus
vv                                 16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       4                117
  WHITE                                          22                697
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V14, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     0  18
  16Q LOSS WILD-TYPE  42 604
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      0   18
  16Q LOSS WILD-TYPE   42  604
                        clus
vv                       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    0                 42
  NOT HISPANIC OR LATINO               18                604
[1] 2 2
[1] FALSE

Clustering(71) Variable = 17P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  17P LOSS MUTATED    77  33
  17P LOSS WILD-TYPE 571 195
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               110                766 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                33                195 
$`17P LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B0-4707 TCGA-B0-4712 
      102.81        28.11        47.24       130.13        19.73        43.96 
TCGA-DV-5565 TCGA-G6-A8L7 TCGA-BQ-7058 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       43.69        70.13        11.28        38.07       153.73        23.84 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 
      137.06        90.48       108.62        98.96        84.89        96.95 
TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 
       92.55        30.25        44.84        86.56        66.54        24.79 
TCGA-KL-8342 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       73.91        54.74        62.37       151.96        44.91        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       105.47       100.47       103.40        92.71 
TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
       16.67       104.55       105.60        96.62        90.48        92.55 
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3374 TCGA-A3-3382 TCGA-AK-3433 
       49.08        37.15         4.50        43.20        18.87       112.08 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
      109.51        94.19        40.01        37.58        12.13        40.70 
TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-4817 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-5117 
        3.62         0.59        33.50        78.44        40.70        52.87 
TCGA-B0-5702 TCGA-B2-3923 TCGA-B4-5835 TCGA-BP-4166 TCGA-BP-4176 TCGA-BP-4334 
       71.41        32.61         0.53         0.43        64.27        21.21 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4787 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4994 
       31.89        11.31        15.78        36.39        10.98        43.00 
TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-5676 TCGA-CJ-5677 
       33.47        19.82        79.66        47.18       133.71        25.71 
TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5468 
       66.31        69.21         6.77        94.45        84.30         1.94 
TCGA-DV-A4VX TCGA-2Z-A9JI TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-5P-A9KH TCGA-A4-7287 
       53.46        51.52        15.48        19.36        67.43        19.63 
TCGA-A4-7915 TCGA-A4-A57E TCGA-AL-3466 TCGA-G7-6789 TCGA-G7-6793 TCGA-HE-7130 
        0.23         8.48         9.63         4.01        11.05        58.19 
TCGA-J7-A8I2 TCGA-Q2-A5QZ 
       10.09        14.07 

$`17P LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
        0.59       107.54         5.46        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        81.21 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 
       16.18        22.49        12.26        67.17        61.05        21.37 
TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
        0.89        12.99        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 
       21.07        10.16        21.86        11.87        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 
       13.25        11.97        96.92        44.84        26.27        20.12 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 
       15.62         6.74       109.22        98.33        71.41        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       103.10        99.88        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 
       36.82         0.53        39.16        24.16        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        62.01 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ TCGA-A3-A8OV 
       33.47        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-3430 
       10.62        29.10       117.80       122.56       109.41        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 
       73.68        68.61        46.78        48.36        78.64        94.29 
TCGA-AK-3453 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       83.21        38.40        82.45        72.89         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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 
        6.64         3.25        58.45        15.72        46.59         5.52 
TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 
       45.07        16.77         6.02        40.44        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 
       54.48        29.10        10.09        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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       73.84       149.16       105.37       130.65        79.89       131.15 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       89.49        91.46        35.90         1.68        31.96        21.30 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
       31.30        31.66        32.98        21.57        16.67        12.00 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.75         5.10         1.25         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
       85.51        90.28       101.06        93.34        99.85        89.36 
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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 
       53.42        27.78        62.07        37.25        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       12.23        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
        5.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       60.95        48.95        36.53        36.95         6.71        47.97 
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-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-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       24.62        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       72.00       129.40        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 
       83.90        18.77        25.45        47.08        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        69.96        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-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       14.63        22.78        62.63        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       56.81        54.64        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW 
       29.36         5.29         0.13        12.82        11.57       106.55 
TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 
       49.58        90.21        22.26        78.64        71.80        62.93 
TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7583 
       43.04        12.99        12.39        27.09        18.21         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       35.18        19.13         7.82        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 
        8.28        12.46        70.19        49.32        66.71        62.66 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
       67.73         2.20        41.13        37.51        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 
       30.28        25.35        10.82         7.66         0.95         7.92 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        2.76       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 
       49.84         7.63         7.04         7.17         3.81        40.77 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       79.86        80.88        51.19        74.60        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       24.89        10.68        13.08         2.40         1.18         0.43 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
       51.78        90.90        39.25        71.44        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
       25.84        25.25        17.98        23.08        16.90        80.65 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
      194.79        12.92         3.68        27.65         1.05        12.43 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI 
       12.89        11.21        16.31        81.93        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       12.76        10.55        18.41        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
       27.78        30.38        27.65        20.25        17.62        31.13 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
       15.48        99.78        87.09        42.94         6.61        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R 
       92.58        52.27        16.01        50.60        78.90        47.90 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
       49.45        44.61        28.80        27.06        11.93        19.00 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 
       16.31        41.62        26.47        53.10        43.76        18.02 
TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP 
       26.20       117.40       103.63       125.29        37.35        98.96 
TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       86.27        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 
       51.35        31.73        26.01        39.06        18.64        18.64 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.05        25.28         6.02        13.28 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.23               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            153.73             194.79 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             47.21              33.29 
[1] "0.2 - 153.7 (47.2)" "0.1 - 194.8 (33.3)"
[1] "hr=" "1.1"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17P LOSS MUTATED        33       30        24       20
  17P LOSS WILD-TYPE     421       73       166       84
D71V3, multiclass
           clus
vv          17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                 33                421
  STAGE II                30                 73
  STAGE III               24                166
  STAGE IV                20                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P LOSS MUTATED    34  33  41   3
  17P LOSS WILD-TYPE 446  94 217  12
D71V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1               34                446
  T2               33                 94
  T3               41                217
  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    55   4   5
  17P LOSS WILD-TYPE 268  40   1
D71V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               55                268
  N1                4                 40
  N2                5                  1
[1] 3 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    64  15
  17P LOSS WILD-TYPE 482  74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     64   15
  17P LOSS WILD-TYPE  482   74
   clus
vv  17P LOSS MUTATED 17P LOSS WILD-TYPE
  0               64                482
  1               15                 74
[1] 2 2
[1] FALSE
D71V7, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    42  69
  17P LOSS WILD-TYPE 250 521
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     42   69
  17P LOSS WILD-TYPE  250  521
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               42                250
  MALE                 69                521
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  17P LOSS MUTATED    69   0
  17P LOSS WILD-TYPE 339   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     69    0
  17P LOSS WILD-TYPE  339    3
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                69                339
  YES                0                  3
[1] 2 2
[1] FALSE
D71V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17P LOSS MUTATED                   50                                47
  17P LOSS WILD-TYPE                 16                               481
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17P LOSS MUTATED                                      14
  17P LOSS WILD-TYPE                                   274
D71V10, multiclass
                                       clus
vv                                      17P LOSS MUTATED 17P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  50                 16
  KIDNEY CLEAR CELL RENAL CARCINOMA                   47                481
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               14                274
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
D71V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17P LOSS MUTATED                                  0     3
  17P LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED                          10    94
  17P LOSS WILD-TYPE                       111   625
D71V13, multiclass
                                  clus
vv                                 17P LOSS MUTATED 17P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 13
  BLACK OR AFRICAN AMERICAN                      10                111
  WHITE                                          94                625
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V14, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4  65
  17P LOSS WILD-TYPE  38 557
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4   65
  17P LOSS WILD-TYPE   38  557
                        clus
vv                       17P LOSS MUTATED 17P LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               65                557
[1] 2 2
[1] FALSE

Clustering(72) Variable = 17Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    64  17
  17Q LOSS WILD-TYPE 584 211
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                81                795 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                17                211 
$`17Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-B0-4712 TCGA-KL-8323 
      102.81        28.11        47.24       130.13        43.96        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
      153.73        23.84       137.06        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 
       84.89        96.95        92.55        30.25        44.84        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       66.54        24.79        73.91        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 
       44.91        49.97       123.12       129.37        87.91        25.48 
TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
       65.19       104.52         0.99        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       105.47       100.47 
TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 
      103.40        92.71        16.67       104.55       105.60        96.62 
TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3374 
       90.48        92.55        49.08        37.15         4.50        43.20 
TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
      112.08       109.51        94.19        40.01        12.13        40.70 
TCGA-B0-4699 TCGA-B0-4817 TCGA-B0-4836 TCGA-B0-5117 TCGA-B2-3923 TCGA-BP-4166 
        3.62        33.50        40.70        52.87        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-5460 TCGA-CZ-5465 
       33.47        79.66       133.71        66.31        94.45        84.30 
TCGA-5P-A9KH TCGA-A4-A57E TCGA-J7-A8I2 
       67.43         8.48        10.09 

$`17Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       19.73        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 
       70.68       119.38       126.05        24.82        25.91         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 
        8.42        15.42       111.02        94.72        32.61         3.58 
TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 
       80.68        74.17        54.77        12.33        77.62        44.15 
TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 
       60.59        11.64        20.38        37.25         6.94        61.51 
TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       53.65        25.81        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 
       31.79        44.55        31.27        63.25       105.37        26.93 
TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 
       27.65       108.56        53.26       118.85        75.58       103.43 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 
       46.16         0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD 
       23.90        81.21        70.13        23.01        75.42        34.85 
TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       39.88        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 
       49.25        21.67        27.68        21.07        10.16        21.86 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8326 TCGA-KL-8333 TCGA-KL-8343 TCGA-KL-8344 TCGA-KM-8477 TCGA-KM-8639 
      109.22        98.33        71.41        28.80        51.06        31.33 
TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8426 TCGA-KN-8433 TCGA-KN-8437 TCGA-KO-8404 
       23.47        25.91         3.55        11.21       100.87        10.68 
TCGA-KO-8410 TCGA-KO-8413 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 
      103.10        99.88        12.66        11.90        36.82         0.53 
TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       39.16        24.16        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3349 
       38.99        37.38        48.82        62.01        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
       68.61        46.78        48.36        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        82.45        72.89         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        57.70 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        58.45        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
        5.52        45.07        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-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       52.73        41.88        51.02        38.43        48.82        46.39 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       56.98        42.41       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
      130.65        79.89       131.15        89.49        91.46        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
      101.06        93.34        99.85        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
       27.78        62.07        37.25        15.62         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       18.48        52.24        62.86        49.08        44.94        12.23 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       15.78        48.95        36.53        36.95         6.71        47.97 
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-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-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       24.62        19.82        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        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       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5678 
       18.81       131.08        72.00       129.40        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 
       47.08        69.21        58.75         6.77        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 
       18.44        79.63        90.54        91.69        55.33        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        69.96        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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 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-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N 
       62.66        67.73         2.20        41.13        37.51        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
       14.86        17.49        12.30        86.76        19.27         8.88 
TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 
       63.72        22.92        43.20        47.80        21.63        40.83 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       26.04        30.28        25.35        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 
        7.92         2.76       123.62        48.26        93.34        61.28 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
       50.40        49.84         7.63         7.04         7.17         3.81 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 
       40.77        79.86        80.88        51.19        74.60        34.19 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
       19.00        24.89        10.68        13.08         2.40         1.18 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
        0.43         4.01        51.78        90.90        11.05        39.25 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       71.44        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       23.08        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
      117.40       103.63       125.29        37.35        98.96        86.27 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 
       71.24        30.67        47.47        65.13       110.73        51.35 
TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 
       31.73        26.01        39.06        18.64        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       25.28         6.02        13.28 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.43               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
            153.73             194.79 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             59.08              32.61 
[1] "0.4 - 153.7 (59.1)" "0.1 - 194.8 (32.6)"
[1] "hr=" "1.9"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  17Q LOSS MUTATED        24       27        17       12
  17Q LOSS WILD-TYPE     430       76       173       92
D72V3, multiclass
           clus
vv          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                 24                430
  STAGE II                27                 76
  STAGE III               17                173
  STAGE IV                12                 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
  17Q LOSS MUTATED    25  29  26   2
  17Q LOSS WILD-TYPE 455  98 232  13
D72V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1               25                455
  T2               29                 98
  T3               26                232
  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 LOSS MUTATED    45   3   2
  17Q LOSS WILD-TYPE 278  41   4
D72V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               45                278
  N1                3                 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"
D72V6, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    50  10
  17Q LOSS WILD-TYPE 496  79
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     50   10
  17Q LOSS WILD-TYPE  496   79
   clus
vv  17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  0               50                496
  1               10                 79
[1] 2 2
[1] FALSE
D72V7, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    30  52
  17Q LOSS WILD-TYPE 262 538
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     30   52
  17Q LOSS WILD-TYPE  262  538
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               30                262
  MALE                 52                538
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    59   0
  17Q LOSS WILD-TYPE 349   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     59    0
  17Q LOSS WILD-TYPE  349    3
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                59                349
  YES                0                  3
[1] 2 2
[1] FALSE
D72V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  17Q LOSS MUTATED                   50                                29
  17Q LOSS WILD-TYPE                 16                               499
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  17Q LOSS MUTATED                                       3
  17Q LOSS WILD-TYPE                                   285
D72V10, multiclass
                                       clus
vv                                      17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  50                 16
  KIDNEY CLEAR CELL RENAL CARCINOMA                   29                499
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                3                285
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
D72V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  17Q LOSS MUTATED                                  0     3
  17Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED                           5    71
  17Q LOSS WILD-TYPE                       116   648
D72V13, multiclass
                                  clus
vv                                 17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 13
  BLACK OR AFRICAN AMERICAN                       5                116
  WHITE                                          71                648
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V14, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     4  42
  17Q LOSS WILD-TYPE  38 580
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      4   42
  17Q LOSS WILD-TYPE   38  580
                        clus
vv                       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               42                580
[1] 2 2
[1] FALSE

Clustering(73) Variable = 18P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED    81  58
  18P LOSS WILD-TYPE 567 170
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               139                737 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                58                170 
$`18P LOSS MUTATED`
TCGA-KL-8328 TCGA-AK-3425 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B8-4621 
      102.81       109.91        19.73        43.96        52.21        25.91 
TCGA-BP-4164 TCGA-BP-4353 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5201 
       32.61        12.33        62.86        49.15        31.79        31.27 
TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-6027 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-AL-A5DJ 
       63.25        26.93       118.85        23.01        39.88        49.25 
TCGA-BQ-7058 TCGA-DW-7840 TCGA-SX-A7SO TCGA-KL-8329 TCGA-KL-8331 TCGA-KL-8336 
       11.28         3.75        41.33        90.48        98.96        30.25 
TCGA-KN-8427 TCGA-KN-8429 TCGA-KO-8404 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 
        0.99        87.12        10.68        37.15         4.50        52.93 
TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 
       88.37        24.16        20.28        15.78       109.51        94.19 
TCGA-AK-3465 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4713 
       12.13         1.38         3.62        65.10         5.98         6.64 
TCGA-B0-4811 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4827 TCGA-B0-4836 
       46.59         6.02        40.44        36.53        29.10        40.70 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4848 TCGA-B0-5092 TCGA-B0-5097 TCGA-B2-4098 
       10.29        65.29        29.03        15.09        21.86         1.68 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-5163 TCGA-B8-5549 
       21.57         5.10         0.53        25.55        27.02         6.38 
TCGA-B8-5550 TCGA-BP-4166 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4343 TCGA-BP-4352 
       48.53         0.43        93.99        18.48        62.86        11.31 
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-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4637 TCGA-CJ-4873 
       30.64        33.47        19.82        34.95        73.22        74.27 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4888 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4920 
       66.21        61.91        51.52        47.67        49.28         4.57 
TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CZ-4857 TCGA-CZ-4858 
       25.71        22.32        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       107.41        79.63         1.94        67.96 
TCGA-CZ-5985 TCGA-CZ-5988 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JP TCGA-4A-A93X 
       65.65        22.78        54.64        51.52        29.36        12.82 
TCGA-5P-A9JW TCGA-5P-A9K3 TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A57E 
      106.55        15.48        19.36        18.21        25.64         8.48 
TCGA-B1-7332 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 
       37.51        20.32        29.03        20.61         8.88        22.92 
TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7059 
       21.63        25.35         2.76       123.62        93.34         7.63 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-GL-7773 TCGA-GL-7966 
       24.89        10.68        13.08         4.01        12.92         3.68 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-Q2-A5QZ TCGA-SX-A7SM 
        2.04        10.55         6.61        16.01        14.07        11.93 
TCGA-Y8-A8S1 
       13.28 

$`18P LOSS WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
       28.11        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 
       38.47        34.29        31.07        42.97        82.32        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       28.73        22.45        18.51       112.80       133.94        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 TCGA-B8-A54H 
       70.68       119.38       126.05        24.82         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
       15.42       111.02        94.72         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 
       54.77        77.62        44.15        60.59        11.64        20.38 
TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 
       37.25         6.94        61.51        53.65        25.81        27.22 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 
        5.82        45.07        41.62        27.62        35.90        48.10 
TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 
       27.02        44.55       105.37        27.65       108.56        53.26 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-2Z-A9J9 
       66.28        56.84        23.90        81.21        70.13        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       34.85        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 
       67.17        61.05        21.37         0.89        12.99        76.64 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       26.27        20.12        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 
       37.55        24.46        13.78        14.63         3.02        61.02 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
       17.95        84.89        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       19.73        17.75        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      137.06       108.62        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-KL-8346 TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 
       28.80        54.74        62.37       151.96        44.91        49.97 
TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 
      123.12        51.06        31.33       129.37        23.47        87.91 
TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 
       25.48        25.91        65.19       104.52         3.55        52.27 
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-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      100.87       105.47       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       92.55        12.66        11.90        36.82         0.53        39.16 
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       24.16        49.08        49.02        49.58        48.59        36.36 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3349 TCGA-A3-3351 
       38.99        37.38        48.82        62.01        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       18.44        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       28.31        65.52        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 
      109.41        73.68       112.08        68.61        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
       78.64        40.01        94.29        83.21        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
       82.45        72.89        40.70         1.41         3.32         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4701 
        4.57         2.53         3.48        28.47        19.00         7.82 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 
        2.14        57.70         3.25        58.45        15.72         0.59 
TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 TCGA-B0-4824 
        5.52        45.07        33.50        16.77        14.93        54.48 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        68.71        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4849 
        6.71        56.68        10.52        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-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 
        7.30        25.32        10.95         8.05         2.24        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR 
       31.96        21.30        31.30        31.66        32.98        16.67 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
       12.00         5.75         1.25         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5164 
       45.37        17.19        50.14        40.04        23.74         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       24.23        50.14        16.60         0.53        34.39        14.30 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        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-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4341 TCGA-BP-4346 
       37.25        21.21        15.62         0.07        52.24        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 
       44.94        12.23        31.89        33.99        31.33        72.59 
TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 
       77.98        41.75        71.80        48.07        13.15        61.68 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4787 
        5.33        61.97        13.51        56.91        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 
       48.95        36.53        10.98        36.95        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       71.41        63.62        60.30        61.22         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         6.94 
TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 
       47.11        36.07        33.34        46.45        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       46.45        16.47        30.64        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       35.21        28.87        79.30         2.04        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        46.55        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       79.66        47.18        75.06       116.84        64.27        71.87 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 
       57.83       113.46        64.18        30.64        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-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-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
       45.14         3.06        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
      133.71        18.87        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       73.35        67.00        62.66       119.64         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-6097 TCGA-CZ-4853 
       74.66         1.35       105.93        83.90        18.77        25.45 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       58.75        14.66        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5987 
        2.40        31.10        12.69        80.19        12.26        14.63 
TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 
       19.96        16.37        11.70         7.04        75.55        59.01 
TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       58.22       100.27        56.91         4.57        91.73        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JR TCGA-4A-A93W 
       38.99        30.71        24.33        31.20         5.29         0.13 
TCGA-4A-A93Y TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K4 
       11.57        49.58        90.21        22.26        78.64        71.80 
TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH 
       62.93        43.04        12.99        12.39        27.09        67.43 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       19.63         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 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-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       16.31        15.75         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
       36.49        20.25        16.77        33.83        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       12.46        50.50        28.18        26.40         0.46         1.15 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
       43.99        22.06        17.23         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       12.30        86.76        19.27        63.72        43.20        47.80 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 
       40.83        26.04        30.28        10.82         7.66         0.95 
TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 
        7.92        48.26        61.28        50.40        49.84         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G 
       74.60        34.19        19.00         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        90.90        11.05        39.25        71.44        25.15 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD 
       20.52        25.84        25.25        17.98        23.08        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       80.65       194.79        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S 
       56.75        73.25        25.22        16.80        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94        99.12        92.58        52.27 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.64        18.05        25.28         6.02 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.43               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            123.62             194.79 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             25.71              37.25 
[1] "0.4 - 123.6 (25.7)" "0.1 - 194.8 (37.2)"
[1] "hr=" "2.2"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18P LOSS MUTATED        45       10        50       31
  18P LOSS WILD-TYPE     409       93       140       73
D73V3, multiclass
           clus
vv          18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                 45                409
  STAGE II                10                 93
  STAGE III               50                140
  STAGE IV                31                 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
  18P LOSS MUTATED    48  15  71   7
  18P LOSS WILD-TYPE 432 112 187   8
D73V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1               48                432
  T2               15                112
  T3               71                187
  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
  18P LOSS MUTATED    53  13   3
  18P LOSS WILD-TYPE 270  31   3
D73V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               53                270
  N1               13                 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    89  24
  18P LOSS WILD-TYPE 457  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     89   24
  18P LOSS WILD-TYPE  457   65
   clus
vv  18P LOSS MUTATED 18P LOSS WILD-TYPE
  0               89                457
  1               24                 65
[1] 2 2
[1] FALSE
D73V7, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    47  94
  18P LOSS WILD-TYPE 245 496
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     47   94
  18P LOSS WILD-TYPE  245  496
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               47                245
  MALE                 94                496
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED    46   0
  18P LOSS WILD-TYPE 362   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     46    0
  18P LOSS WILD-TYPE  362    3
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                46                362
  YES                0                  3
[1] 2 2
[1] FALSE
D73V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18P LOSS MUTATED                    8                                93
  18P LOSS WILD-TYPE                 58                               435
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18P LOSS MUTATED                                      40
  18P LOSS WILD-TYPE                                   248
D73V10, multiclass
                                       clus
vv                                      18P LOSS MUTATED 18P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   8                 58
  KIDNEY CLEAR CELL RENAL CARCINOMA                   93                435
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               40                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"
D73V11, continuous
D73V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18P LOSS MUTATED                                  0     5
  18P LOSS WILD-TYPE                                2    11
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED                          13   121
  18P LOSS WILD-TYPE                       108   598
D73V13, multiclass
                                  clus
vv                                 18P LOSS MUTATED 18P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           5                 11
  BLACK OR AFRICAN AMERICAN                      13                108
  WHITE                                         121                598
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V14, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     3  96
  18P LOSS WILD-TYPE  39 526
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      3   96
  18P LOSS WILD-TYPE   39  526
                        clus
vv                       18P LOSS MUTATED 18P LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO               96                526
[1] 2 2
[1] FALSE

Clustering(74) Variable = 18Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED    87  59
  18Q LOSS WILD-TYPE 561 169
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               146                730 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                59                169 
$`18Q LOSS MUTATED`
TCGA-KL-8328 TCGA-AK-3425 TCGA-B0-4712 TCGA-B0-4815 TCGA-B8-4621 TCGA-BP-4164 
      102.81       109.91        43.96        52.21        25.91        32.61 
TCGA-BP-4353 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4636 
       12.33        62.86        49.15        31.79        31.27        63.25 
TCGA-CJ-4891 TCGA-CJ-6027 TCGA-CZ-4854 TCGA-MM-A84U TCGA-2Z-A9JJ TCGA-A4-A5Y1 
       26.93       118.85        46.16        23.01        39.88        12.99 
TCGA-AL-A5DJ TCGA-BQ-7058 TCGA-DW-7840 TCGA-SX-A7SO TCGA-KL-8329 TCGA-KL-8331 
       49.25        11.28         3.75        41.33        90.48        98.96 
TCGA-KL-8336 TCGA-KN-8424 TCGA-KN-8427 TCGA-KN-8429 TCGA-KO-8404 TCGA-A3-3313 
       30.25        65.19         0.99        87.12        10.68        24.16 
TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3372 TCGA-A3-3387 
       37.15         4.50        52.93        88.37        24.16        20.28 
TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-4698 TCGA-B0-4699 
       15.78       109.51        94.19        12.13         1.38         3.62 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4713 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
       65.10         5.98         6.64         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-B0-5121 TCGA-B2-4098 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 
       21.86        48.82         1.68        21.57         5.10         0.53 
TCGA-B8-4620 TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5550 TCGA-BP-4166 TCGA-BP-4338 
       25.55        27.02         6.38        48.53         0.43        93.99 
TCGA-BP-4343 TCGA-BP-4352 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 TCGA-BP-4781 
       62.86        11.31        12.30         5.98        10.82        68.38 
TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4962 TCGA-BP-4977 TCGA-BP-4985 TCGA-BP-4994 
       36.39         6.71        58.68        14.93        31.30        43.00 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5182 TCGA-BP-5196 TCGA-BP-5198 
       18.51         6.35        30.64        38.30        33.47        19.82 
TCGA-BP-5200 TCGA-CJ-4637 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4888 
       34.95        73.22        47.18        74.27        66.21        51.52 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4920 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-6028 
       47.67        49.28         4.57        25.71        22.32        53.42 
TCGA-CJ-6032 TCGA-CW-5588 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4860 TCGA-CZ-4863 
      119.64        66.31        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 
      107.41        79.63         1.94        67.96        65.65        22.78 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JP TCGA-4A-A93X TCGA-5P-A9JW TCGA-5P-A9K3 
       54.64        51.52        29.36        12.82       106.55        15.48 
TCGA-5P-A9K9 TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-A57E TCGA-B1-7332 TCGA-B1-A656 
       19.36        18.21        25.64         8.48        37.51        20.32 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 
       29.03        20.61         8.88        22.92        21.63        25.35 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7059 TCGA-EV-5903 TCGA-F9-A4JJ 
        2.76       123.62        93.34         7.63        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 
       13.08         0.43         4.01        16.90        12.92         3.68 
TCGA-HE-7130 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EA TCGA-Q2-A5QZ TCGA-SX-A7SM 
       58.19         2.04        10.55         6.61        14.07        11.93 
TCGA-UZ-A9PQ TCGA-Y8-A8S1 
       86.27        13.28 

$`18Q LOSS WILD-TYPE`
TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
       28.11        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3450 
       38.47        34.29        31.07        42.97        82.32        58.49 
TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       28.73        22.45        19.73        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-5162 
       15.78        70.68       119.38       126.05        24.82         1.18 
TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 
        8.42        15.42       111.02        94.72         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       74.17        54.77        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5189 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-4904 
       48.10        27.02        44.55       105.37        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       53.26        75.58       103.43         0.59       107.54         5.46 
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-G6-A8L7 TCGA-2Z-A9J9 
       66.28        56.84        23.90        81.21        70.13        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU 
       34.85        33.07        25.58        16.18        22.49        12.26 
TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-B1-A47M 
       67.17        61.05        21.37         0.89        76.64        21.67 
TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B TCGA-B9-A5W7 
       27.68        21.07        10.16        21.86        11.87        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
       20.12        48.85        13.61       129.86        35.93        37.55 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       24.46        13.78        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       17.75        62.83        86.37        21.60        15.91        15.62 
TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 
        6.74        38.07       153.73        23.84       109.22       137.06 
TCGA-KL-8330 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8337 
      108.62        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-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 
       54.74        62.37       151.96        44.91        49.97       123.12 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 
       51.06        31.33       129.37        23.47        87.91        25.48 
TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8428 TCGA-KN-8431 TCGA-KN-8432 
       25.91       104.52         3.55        52.27        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
       99.88       105.60        96.62        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 
       11.90        36.82         0.53        39.16        49.08        49.02 
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-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3362 TCGA-A3-3363 
       62.01        45.53        29.92        18.44        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-A6NI 
       20.71        18.64        18.87        28.31        65.52        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 
       29.10       117.80       122.56       109.41        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       68.61        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3777 
       83.21        37.58        38.40        82.45        72.89        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-B0-4701 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4714 
       28.47        19.00         7.82         2.14        57.70         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4823 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 
       10.52        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-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
       66.05        38.63        52.73        41.88        52.87        51.02 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       38.43        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
       85.78        86.47       126.28        80.91        71.41        73.84 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
      149.16       105.37       130.65        79.89       131.15        89.49 
TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       91.46        32.61        35.90        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
       31.66        32.98        16.67        12.00         5.75         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-B8-4622 
       49.97        42.71        25.05        45.37        17.19        50.14 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       40.04        23.74         0.85        24.23        50.14        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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 
        1.74         4.93        17.36        16.27        14.17        85.51 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
       90.28       101.06        93.34        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-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
        0.07        18.48        52.24        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 
       31.89        33.99        31.33        72.59        77.98        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-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       13.51        56.91        60.95        15.78        48.95        36.53 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
       10.98        36.95        47.97        87.45        71.41        63.62 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4981 
       48.89        49.38        45.50         6.94        47.11        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       33.34        46.45        36.95         3.88        46.45        16.47 
TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 
       30.64        38.70        37.02        37.48        35.21        28.87 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
       79.30         2.04        74.20        52.27         9.63        74.40 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       42.44        37.25        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       23.47        13.41        24.62         0.95       115.00        46.55 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        83.97        49.25        79.66        75.06       116.84 
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       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       30.64        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
      109.84        50.24        56.35        49.97        51.29        49.18 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4923 
       50.33        54.48        38.56        45.14         3.06        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5680 
      131.08        72.00       129.40       133.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 
       18.15       122.83        62.10        73.35        67.00        62.66 
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-6097 TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4864 TCGA-CZ-5451 
       18.77        25.45        58.75        14.66        93.04        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 
       58.82        79.53        23.74        18.44        90.54        91.69 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 
       55.33        94.45        10.85        10.22        21.76        69.96 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       84.30        22.52         2.40        31.10        12.69        80.19 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       12.26        14.63        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO 
       91.73        56.81        38.99        30.71        24.33        31.20 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        5.29         0.13        11.57        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 
       27.09        67.43        19.63         0.10        35.18        19.13 
TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 
        7.82         0.23        16.64        30.48        29.46        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-A6HP 
       12.46        16.96        16.31        15.75         8.28        12.46 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        9.63        70.19        49.32        66.71        62.66        67.73 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B3-3925 
        2.20        41.13        36.49        20.25        16.77        33.83 
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-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
       14.86        17.49        12.30        86.76        19.27        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5889 
       43.20        47.80        40.83        26.04        30.28        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-7045 TCGA-BQ-7050 TCGA-BQ-7051 
        7.66         0.95         7.92        48.26        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
       49.84         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF 
       80.88        51.19        74.60        34.19        19.00         2.40 
TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 
        1.18        51.78        90.90        11.05        39.25        71.44 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       25.15        20.52        25.84        25.25        17.98        23.08 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       80.65       194.79        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL 
       87.09        42.94        99.12        92.58        52.27        16.01 
TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
       50.60        78.90        47.90        49.45        44.61        28.80 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       27.06        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       37.35        98.96        71.24        30.67        47.47        65.13 
TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
      110.73        51.35        31.73        26.01        39.06        18.64 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        18.05        25.28         6.02 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.43               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            123.62             194.79 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            26.975             37.235 
[1] "0.4 - 123.6 (27.0)" "0.1 - 194.8 (37.2)"
[1] "hr=" "2.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  18Q LOSS MUTATED        50       11        51       31
  18Q LOSS WILD-TYPE     404       92       139       73
D74V3, multiclass
           clus
vv          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                 50                404
  STAGE II                11                 92
  STAGE III               51                139
  STAGE IV                31                 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
  18Q LOSS MUTATED    54  17  70   7
  18Q LOSS WILD-TYPE 426 110 188   8
D74V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1               54                426
  T2               17                110
  T3               70                188
  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    57  16   3
  18Q LOSS WILD-TYPE 266  28   3
D74V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               57                266
  N1               16                 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    93  24
  18Q LOSS WILD-TYPE 453  65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     93   24
  18Q LOSS WILD-TYPE  453   65
   clus
vv  18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  0               93                453
  1               24                 65
[1] 2 2
[1] FALSE
D74V7, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    49  99
  18Q LOSS WILD-TYPE 243 491
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     49   99
  18Q LOSS WILD-TYPE  243  491
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               49                243
  MALE                 99                491
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED    52   0
  18Q LOSS WILD-TYPE 356   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     52    0
  18Q LOSS WILD-TYPE  356    3
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                52                356
  YES                0                  3
[1] 2 2
[1] FALSE
D74V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  18Q LOSS MUTATED                    9                                95
  18Q LOSS WILD-TYPE                 57                               433
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  18Q LOSS MUTATED                                      44
  18Q LOSS WILD-TYPE                                   244
D74V10, multiclass
                                       clus
vv                                      18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   9                 57
  KIDNEY CLEAR CELL RENAL CARCINOMA                   95                433
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               44                244
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
D74V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  18Q LOSS MUTATED                                  0     6
  18Q LOSS WILD-TYPE                                2    10
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED                          14   125
  18Q LOSS WILD-TYPE                       107   594
D74V13, multiclass
                                  clus
vv                                 18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           6                 10
  BLACK OR AFRICAN AMERICAN                      14                107
  WHITE                                         125                594
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V14, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     3 101
  18Q LOSS WILD-TYPE  39 521
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      3  101
  18Q LOSS WILD-TYPE   39  521
                        clus
vv                       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    3                 39
  NOT HISPANIC OR LATINO              101                521
[1] 2 2
[1] FALSE

Clustering(75) Variable = 19P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    15  14
  19P LOSS WILD-TYPE 633 214
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                29                847 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                14                214 
$`19P LOSS MUTATED`
TCGA-AK-3425 TCGA-B0-4707 TCGA-BP-4164 TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-KO-8415 
      109.91        19.73        32.61        12.99        11.87        96.62 
TCGA-A3-3319 TCGA-B0-4690 TCGA-B0-4696 TCGA-B0-4821 TCGA-B0-4828 TCGA-B0-5084 
       37.15         1.41        28.47        40.44        10.09         7.30 
TCGA-BP-4770 TCGA-BP-4985 TCGA-CZ-4860 TCGA-2Z-A9JG TCGA-5P-A9KC TCGA-A4-7286 
       10.82        31.30         6.77        54.64        12.39        18.21 
TCGA-A4-8310 TCGA-B1-7332 TCGA-BQ-5876 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 
       25.64        37.51        19.27         0.95         4.01        25.84 
TCGA-G7-A8LD TCGA-IA-A40Y TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-UZ-A9PN 
       16.90         2.04        99.12        14.07        37.35 

$`19P LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 
       58.49        28.73        22.45        43.96        52.21        18.51 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 
      112.80       133.94        15.78        70.68       119.38       126.05 
TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 
       24.82        25.91         1.18         8.42        15.42       111.02 
TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       94.72         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 
       77.62        44.15        60.59        11.64        20.38        37.25 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 
        6.94        61.51        53.65        25.81        27.22         5.82 
TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 
       45.07        41.62        27.62        35.90        48.10        62.86 
TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 
       49.15        27.02        31.79        44.55        31.27        63.25 
TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 
      105.37        26.93        27.65       108.56        53.26       118.85 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       21.86        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 
      108.62        98.96        84.89        98.33        96.95        92.55 
TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8342 
       30.25        44.84        86.56        66.54        24.79        73.91 
TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8440 
       71.41        28.80        54.74        62.37       151.96        44.91 
TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 
       49.97       123.12        51.06        31.33       129.37        23.47 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8426 
       87.91        25.48        25.91        65.19       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8433 
        0.99        52.27        87.12        19.33         2.50        11.21 
TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       99.88       105.60        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         0.53        39.16        24.16        49.08        49.02 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80       122.56       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61       109.51        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         3.32         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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4833 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-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 
       20.94        43.30        11.24        11.90        25.32        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
       10.95         8.05         2.24        21.86        52.08        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        58.59 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
       19.30        66.05        38.63        52.73        41.88        52.87 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
       51.02        38.43        48.82        46.39        56.98        42.41 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
      111.52       129.67        85.78        86.47       126.28        80.91 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
       71.41        73.84       149.16       105.37       130.65        79.89 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
      131.15        89.49        91.46        32.61        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       14.30        27.29        29.88        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 
       93.99        18.48        52.24        62.86        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       13.15        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 
       10.98        36.95         6.71        47.97        87.45        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
       47.11        14.93        36.07        33.34        46.45        36.95 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 
        3.88        46.45        16.47        43.00        30.64        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       13.35        33.24        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 
       19.82        34.95         0.95       115.00        46.55        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17       106.16       114.41        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       21.24        83.97        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06       116.84        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
      115.69        50.01        24.66        39.45       109.84        50.24 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 
       56.35        47.67        49.97        51.29        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       73.35        67.00        53.42        62.66       119.64         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       18.77        25.45        47.08        69.21        58.75        14.66 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39        93.04       107.41        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        79.63        90.54        91.69        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
       94.45        10.85        10.22        21.76        69.96        84.30 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       53.46        12.00        18.12         3.91         6.77         4.18 
TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 
        7.96        10.29        35.87         2.01        19.43        19.96 
TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 
       16.37        11.70         7.04        75.55        59.01        58.22 
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JI 
      100.27        56.91         4.57        91.73        56.81        51.52 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ 
        0.13        12.82        11.57       106.55        49.58        90.21 
TCGA-5P-A9K0 TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 
       22.26        78.64        15.48        71.80        62.93        43.04 
TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 
       19.36        12.99        27.09        67.43        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
       29.46        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-3471 
       15.75         8.28        12.46         9.63        70.19        49.32 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N 
       66.71        62.66        67.73         2.20        41.13        36.49 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
       20.25        16.77        20.32        33.83        29.03        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-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-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35        10.82         7.66         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 
       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 
       90.90        11.05        39.25        71.44        25.15        20.52 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        23.08        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       16.31        81.93        58.19        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
       73.25        25.22        16.80        19.99        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
       96.69        22.26        21.34        12.36        12.76        10.55 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVK 
       99.78        87.09        42.94         6.61        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  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 
             19.27              36.53 
[1] "0.9 - 109.9 (19.3)" "0.1 - 194.8 (36.5)"
[1] "hr=" "2.9"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19P LOSS MUTATED         7        1        13        6
  19P LOSS WILD-TYPE     447      102       177       98
D75V3, multiclass
           clus
vv          19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                  7                447
  STAGE II                 1                102
  STAGE III               13                177
  STAGE IV                 6                 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
  19P LOSS MUTATED     9   2  15   3
  19P LOSS WILD-TYPE 471 125 243  12
D75V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                9                471
  T2                2                125
  T3               15                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
  19P LOSS MUTATED     8   4   1
  19P LOSS WILD-TYPE 315  40   5
D75V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0                8                315
  N1                4                 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    11   4
  19P LOSS WILD-TYPE 535  85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     11    4
  19P LOSS WILD-TYPE  535   85
   clus
vv  19P LOSS MUTATED 19P LOSS WILD-TYPE
  0               11                535
  1                4                 85
[1] 2 2
[1] FALSE
D75V7, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    10  19
  19P LOSS WILD-TYPE 282 571
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10   19
  19P LOSS WILD-TYPE  282  571
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               10                282
  MALE                 19                571
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    14   0
  19P LOSS WILD-TYPE 394   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     14    0
  19P LOSS WILD-TYPE  394    3
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                14                394
  YES                0                  3
[1] 2 2
[1] FALSE
D75V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19P LOSS MUTATED                    1                                12
  19P LOSS WILD-TYPE                 65                               516
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19P LOSS MUTATED                                      16
  19P LOSS WILD-TYPE                                   272
D75V10, multiclass
                                       clus
vv                                      19P LOSS MUTATED 19P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   1                 65
  KIDNEY CLEAR CELL RENAL CARCINOMA                   12                516
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               16                272
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
D75V12, continuous
[1] "Remove cluster labels:" "19P LOSS MUTATED"      
clus
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 2                 72 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B2-A4SR         TCGA-B8-5158         TCGA-B8-5550 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J3 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-2Z-A9J7         TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-7501 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-G7-A8LB         TCGA-G7-A8LE         TCGA-GL-7773 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-GL-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-SX-A71S         TCGA-SX-A71U 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SR 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-UZ-A9PM         TCGA-UZ-A9PS 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-UZ-A9PX         TCGA-WN-A9G9         TCGA-WN-AB4C 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" "19P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19P LOSS MUTATED                                  0     1
  19P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED                           3    25
  19P LOSS WILD-TYPE                       118   694
D75V13, multiclass
                                  clus
vv                                 19P LOSS MUTATED 19P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       3                118
  WHITE                                          25                694
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V14, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  22
  19P LOSS WILD-TYPE  41 600
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   22
  19P LOSS WILD-TYPE   41  600
                        clus
vv                       19P LOSS MUTATED 19P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               22                600
[1] 2 2
[1] FALSE

Clustering(76) Variable = 19Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    13  10
  19Q LOSS WILD-TYPE 635 218
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                23                853 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                10                218 
$`19Q LOSS MUTATED`
TCGA-BP-4164 TCGA-A4-A5Y1 TCGA-B9-A44B TCGA-KL-8341 TCGA-KN-8427 TCGA-KO-8415 
       32.61        12.99        11.87        24.79         0.99        96.62 
TCGA-A3-3319 TCGA-B0-4690 TCGA-B0-5084 TCGA-CZ-4860 TCGA-2Z-A9JG TCGA-2Z-A9JI 
       37.15         1.41         7.30         6.77        54.64        51.52 
TCGA-A4-7286 TCGA-A4-8310 TCGA-B1-7332 TCGA-BQ-5891 TCGA-F9-A4JJ TCGA-G7-6789 
       18.21        25.64        37.51         0.95        10.68         4.01 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Q2-A5QZ TCGA-UZ-A9PN 
       25.84        16.90         2.04        14.07        37.35 

$`19Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 
       15.42       111.02        94.72         3.58        80.68        74.17 
TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 
       54.77        12.33        77.62        44.15        60.59        11.64 
TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4986 
       20.38        37.25         6.94        61.51        53.65        25.81 
TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 TCGA-BP-5009 
       27.22         5.82        45.07        41.62        27.62        35.90 
TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5199 
       48.10        62.86        49.15        27.02        31.79        44.55 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 TCGA-CJ-4904 
       31.27        63.25       105.37        26.93        27.65       108.56 
TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
       53.26       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 
       25.58        16.18        22.49        12.26        67.17        61.05 
TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       21.37         0.89        76.64        49.25        21.67        27.68 
TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 
       21.07        10.16        21.86        19.23        26.04        13.25 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
       11.97        96.92        44.84        26.27        20.12        11.28 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
       48.85        13.61       129.86        35.93        37.55        24.46 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T 
       13.78         3.75        14.63         3.02        61.02        17.95 
TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 
       84.89        67.17        16.34        12.13        29.26        19.73 
TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       17.75        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 
       15.62         6.74        38.07       153.73        23.84       109.22 
TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
      137.06        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 TCGA-KM-8438 
       73.91        71.41        28.80        54.74        62.37       151.96 
TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 
       44.91        49.97       123.12        51.06        31.33       129.37 
TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
       23.47        87.91        25.48        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-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-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 TCGA-KO-8404 
       59.08       115.00        42.35       100.87       105.47        10.68 
TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 TCGA-KO-8410 
      100.47       103.40        92.71        16.67       104.55       103.10 
TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E 
       99.88       105.60        90.48        92.55        12.66        11.90 
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       36.82         0.53        39.16        24.16        49.08        49.02 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A6NI TCGA-A3-A6NJ 
       18.87        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80       122.56       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
       68.61       109.51        94.19        46.78        48.36        78.64 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       40.01        94.29        83.21        37.58        38.40        82.45 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4691 
       72.89        12.13        40.70         1.41         3.32         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-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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 
       10.52        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       11.90        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97        87.45        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 
       36.07        33.34        46.45        31.30        36.95         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       46.45        16.47        43.00        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.02        37.48        35.21        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        2.04        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       33.24        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
      131.08        72.00       129.40       133.71        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15       122.83        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       67.00        53.42        62.66       119.64         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-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-6097 
       78.18        74.66         1.35       105.93        83.90        18.77 
TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 
       25.45        47.08        69.21        58.75        14.66        63.39 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
       93.04       107.41        63.42        58.82        79.53        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        79.63        90.54        91.69        55.33        94.45 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
       10.85        10.22        21.76        69.96        84.30        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       65.65        12.26        14.63        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
       12.00        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-MW-A4EC 
       10.29        35.87         2.01        19.43        19.96        16.37 
TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 
       11.70         7.04        75.55        59.01        58.22       100.27 
TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM 
       56.91         4.57        91.73        56.81        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.39        27.09        67.43        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8311 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-3471 TCGA-AL-3472 
        8.28        12.46         9.63        70.19        49.32        66.71 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 
       62.66        67.73         2.20        41.13        36.49        20.25 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 
       16.77        20.32        33.83        29.03        30.58        34.49 
TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       12.46        50.50        28.18        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
        1.15        43.99        22.06        17.23         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
       17.49        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
       22.92        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        25.35        10.82         7.66         7.92         2.76 
TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
      123.62        48.26        93.34        61.28        50.40        49.84 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
        7.63         7.04         7.17         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-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        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM 
       11.05        39.25        71.44        25.15        20.52        25.25 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       17.98        23.08        80.65       194.79        12.92         3.68 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
       27.65         1.05        12.43        12.89        11.21        16.31 
TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       81.93        58.19        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V 
       25.22        16.80        19.99        85.78        88.24        96.69 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 
       22.26        21.34        12.36        12.76        10.55        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       26.47        53.10        43.76        18.02        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        98.96        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.95               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             96.62             194.79 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             16.90              36.49 
[1] "0.9 - 96.6 (16.9)"  "0.1 - 194.8 (36.5)"
[1] "hr=" "3.1"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  19Q LOSS MUTATED         4        1        11        6
  19Q LOSS WILD-TYPE     450      102       179       98
D76V3, multiclass
           clus
vv          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                  4                450
  STAGE II                 1                102
  STAGE III               11                179
  STAGE IV                 6                 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
  19Q LOSS MUTATED     5   1  14   3
  19Q LOSS WILD-TYPE 475 126 244  12
D76V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                5                475
  T2                1                126
  T3               14                244
  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   5   2
  19Q LOSS WILD-TYPE 320  39   4
D76V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0                3                320
  N1                5                 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   3
  19Q LOSS WILD-TYPE 541  86
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      5    3
  19Q LOSS WILD-TYPE  541   86
   clus
vv  19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  0                5                541
  1                3                 86
[1] 2 2
[1] FALSE
D76V7, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     8  15
  19Q LOSS WILD-TYPE 284 575
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      8   15
  19Q LOSS WILD-TYPE  284  575
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE                8                284
  MALE                 15                575
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    16   0
  19Q LOSS WILD-TYPE 392   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     16    0
  19Q LOSS WILD-TYPE  392    3
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                16                392
  YES                0                  3
[1] 2 2
[1] FALSE
D76V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  19Q LOSS MUTATED                    3                                 5
  19Q LOSS WILD-TYPE                 63                               523
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  19Q LOSS MUTATED                                      15
  19Q LOSS WILD-TYPE                                   273
D76V10, multiclass
                                       clus
vv                                      19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   3                 63
  KIDNEY CLEAR CELL RENAL CARCINOMA                    5                523
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               15                273
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
D76V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  19Q LOSS MUTATED                                  0     1
  19Q LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED                           4    18
  19Q LOSS WILD-TYPE                       117   701
D76V13, multiclass
                                  clus
vv                                 19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       4                117
  WHITE                                          18                701
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V14, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  16
  19Q LOSS WILD-TYPE  41 606
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   16
  19Q LOSS WILD-TYPE   41  606
                        clus
vv                       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO               16                606
[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 641 223
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                12                864 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                223 
$`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-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8337 TCGA-KL-8340 
       98.96        84.89        98.33        96.95        44.84        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
        2.50        11.21       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 
      103.10        99.88       105.60        96.62        90.48        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         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-A3-3346 TCGA-A3-3347 
       38.99        37.38        48.82        62.01         4.50        52.93 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 
       45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN TCGA-A3-A8CQ 
       20.28        33.47        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       117.80       122.56       109.41 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
       15.78        73.68       112.08        68.61       109.51        94.19 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
       37.58        38.40        82.45        72.89        12.13        40.70 
TCGA-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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
        5.98         2.14        57.70         6.64         3.25        58.45 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       15.72        46.59         0.59         5.52        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 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        10.52        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 TCGA-B0-5085 
       20.94        43.30        11.24        11.90         7.30        25.32 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 
       15.09        10.95         8.05         2.24        21.86        52.08 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 
       15.95        62.89        90.87        90.48        52.54        30.48 
TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
       58.59        19.30        66.05        38.63        52.73        41.88 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       52.87        51.02        38.43        48.82        46.39        56.98 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 
       42.41       111.52       129.67        85.78        86.47       126.28 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
       80.91        71.41        73.84       149.16       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 TCGA-B2-3924 
       79.89       131.15        89.49        91.46        32.61        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 
        1.68        31.96        21.30        31.30        31.66        32.98 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
       21.57        16.67        12.00         5.75         5.10         1.25 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        0.53         4.64         5.46         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-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-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 
        4.93        17.36        16.27        14.17        85.51        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
      101.06        93.34        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
       77.03        62.24        61.78        64.27        54.90        97.45 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
       53.42        27.78        62.07        37.25        21.21        15.62 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
        0.07        93.99        18.48        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       44.94        12.23        31.89        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       72.59        77.98         5.98        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       13.15        61.68        10.82         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 
       36.39        10.98        36.95         6.71        47.97        87.45 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       71.41        63.62        60.30        61.22         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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       38.70        37.02        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 
       74.40        42.44        37.22        22.78        13.35        33.24 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        0.95       115.00        46.55        14.17       106.16       114.41 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
       54.61        58.95        11.05        21.24        83.97        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06       116.84        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83       113.46        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
       30.64        51.52        63.98       115.69        50.01        24.66 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 
       39.45       109.84        50.24        56.35        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.29        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81       131.08        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
      129.40       133.71        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 
        1.35       105.93        83.90        18.77        25.45        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 
       69.21        58.75         6.77        14.66        63.39        93.04 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
      107.41        63.42        58.82        79.53        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       79.63        90.54        91.69        55.33        94.45        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ 
       12.26        14.63        22.78        62.63        53.46        12.00 
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-MW-A4EC TCGA-T7-A92I 
       35.87         2.01        19.43        19.96        16.37        11.70 
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 
        7.04        75.55        59.01        58.22       100.27        56.91 
TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK 
        4.57        91.73        56.81        54.64        51.52        38.99 
TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W 
       30.71        24.33        31.20        29.36         5.29         0.13 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
       12.82        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 
       12.99        12.39        27.09        67.43        18.21        19.63 
TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
        0.10        35.18        19.13         7.82         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
       30.48        29.46        25.64        23.97        23.28        23.31 
TCGA-A4-8516 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-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
       41.13        37.51        36.49        20.25        16.77        20.32 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
       33.83        29.03        30.58        34.49        12.46        50.50 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 
       28.18        26.40        20.61         0.46         1.15        43.99 
TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
       22.06        17.23         0.16        14.86        17.49        12.30 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       86.76        19.27         8.88        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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              35.54 
[1] "11.3 - 92.5 (39.4)" "0.1 - 194.8 (35.5)"
[1] "hr=" "1.4"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20P LOSS MUTATED         3        2         4        3
  20P LOSS WILD-TYPE     451      101       186      101
D77V3, multiclass
           clus
vv          20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                  3                451
  STAGE II                 2                101
  STAGE III                4                186
  STAGE IV                 3                101
[1] 4 2
[1] TRUE
[1] "dimension of 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 477 124 252  15
D77V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                3                477
  T2                3                124
  T3                6                252
  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 318  43   5
D77V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0                5                318
  N1                1                 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"
D77V6, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     9   2
  20P LOSS WILD-TYPE 537  87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      9    2
  20P LOSS WILD-TYPE  537   87
   clus
vv  20P LOSS MUTATED 20P LOSS WILD-TYPE
  0                9                537
  1                2                 87
[1] 2 2
[1] FALSE
D77V7, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     6   6
  20P LOSS WILD-TYPE 286 584
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      6    6
  20P LOSS WILD-TYPE  286  584
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE                6                286
  MALE                  6                584
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     4   0
  20P LOSS WILD-TYPE 404   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      4    0
  20P LOSS WILD-TYPE  404    3
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 4                404
  YES                0                  3
[1] 2 2
[1] FALSE
D77V9, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                142 
        TCGA-KM-8439         TCGA-KM-8441         TCGA-KM-8442 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8411         TCGA-CZ-4854         TCGA-CZ-4856 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-4862         TCGA-DV-5565         TCGA-DV-5566 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5567         TCGA-DV-5568         TCGA-DV-5569 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5573         TCGA-DV-5574         TCGA-DV-5575 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-5576         TCGA-DV-A4W0         TCGA-G6-A8L7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JL         TCGA-2Z-A9JT         TCGA-5P-A9JU 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-5560         TCGA-DW-5561         TCGA-DW-7834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-7836         TCGA-DW-7837         TCGA-DW-7838 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-7839         TCGA-DW-7840         TCGA-DW-7841 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-7842         TCGA-SX-A7SO         TCGA-UZ-A9PZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8438         TCGA-KM-8440         TCGA-KM-8443 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KM-8476         TCGA-KM-8477         TCGA-KM-8639 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8429         TCGA-KO-8413         TCGA-3Z-A93Z 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-A6NJ         TCGA-A3-A6NL         TCGA-A3-A8CQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3426         TCGA-AK-3428         TCGA-AK-3430 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B0-4838         TCGA-B2-5639         TCGA-B4-5377 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5378         TCGA-B4-5832         TCGA-B4-5834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5835         TCGA-B4-5836         TCGA-B4-5838 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B4-5843         TCGA-B4-5844         TCGA-B8-4143 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-4622         TCGA-B8-5158         TCGA-CJ-6028 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-4858         TCGA-CZ-4860         TCGA-CZ-4861 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5456         TCGA-CZ-5457         TCGA-CZ-5458 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DV-A4VX         TCGA-DV-A4VZ         TCGA-EU-5904 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EU-5905         TCGA-EU-5906         TCGA-EU-5907 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G6-A8L6         TCGA-G6-A8L8         TCGA-T7-A92I 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JE         TCGA-2Z-A9JK         TCGA-2Z-A9JN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-4A-A93W         TCGA-4A-A93X         TCGA-4A-A93Y 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-7286         TCGA-A4-7828         TCGA-A4-8098 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-8311         TCGA-A4-8312 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-8517         TCGA-A4-8518         TCGA-A4-8630 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-A48D         TCGA-A4-A4ZT         TCGA-A4-A57E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-A5DU         TCGA-A4-A5XZ         TCGA-A4-A6HP 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AL-3466         TCGA-DW-7963         TCGA-EV-5901 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-EV-5902         TCGA-EV-5903         TCGA-F9-A7Q0 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-6789         TCGA-G7-6790         TCGA-G7-6792 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-6793         TCGA-G7-6795         TCGA-G7-6796 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-6797         TCGA-G7-7501         TCGA-G7-7502 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-A4TM         TCGA-G7-A8LB         TCGA-G7-A8LC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-A8LD         TCGA-G7-A8LE         TCGA-IA-A40U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IA-A40X         TCGA-IA-A40Y         TCGA-J7-8537 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P4-AAVK         TCGA-Q2-A5QZ         TCGA-SX-A71R 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A71S         TCGA-SX-A71U         TCGA-SX-A71V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A7SL         TCGA-SX-A7SM         TCGA-SX-A7SN 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A7SP         TCGA-SX-A7SQ         TCGA-SX-A7SR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-SX-A7SS         TCGA-SX-A7SU         TCGA-UZ-A9PL 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-V9-A7HT 
"20P LOSS WILD-TYPE" 
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20P LOSS MUTATED                    4                                 7
  20P LOSS WILD-TYPE                 62                               521
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20P LOSS MUTATED                                       1
  20P LOSS WILD-TYPE                                   287
D77V10, multiclass
                                       clus
vv                                      20P LOSS MUTATED 20P LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   4                 62
  KIDNEY CLEAR CELL RENAL CARCINOMA                    7                521
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                1                287
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                105 
        TCGA-B8-4621         TCGA-DV-A4W0         TCGA-G6-A8L7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-KL-8324         TCGA-KL-8330 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8433         TCGA-KO-8408 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416         TCGA-A3-A8CQ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-4146 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-5550 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-G6-A5PC 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J2 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"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-4A-A93W 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9K3         TCGA-5P-A9KE 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-A48D         TCGA-A4-A57E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3466         TCGA-AL-3472 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IA-A83V 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P4-A5EB         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-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
D77V12, continuous
[1] "Remove cluster labels:" "20P LOSS MUTATED"      
clus
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 1                 73 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5550         TCGA-MM-A563 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-T7-A92I         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117         TCGA-B9-A69E 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6793 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-G7-6795         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-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-P4-AAVK         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-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" "20P LOSS WILD-TYPE" 
        TCGA-Y8-A8RY 
"20P LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20P LOSS MUTATED                                  0     1
  20P LOSS WILD-TYPE                                2    15
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED                           0    11
  20P LOSS WILD-TYPE                       121   708
D77V13, multiclass
                                  clus
vv                                 20P LOSS MUTATED 20P LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           1                 15
  BLACK OR AFRICAN AMERICAN                       0                121
  WHITE                                          11                708
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V14, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     1   4
  20P LOSS WILD-TYPE  41 618
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      1    4
  20P LOSS WILD-TYPE   41  618
                        clus
vv                       20P LOSS MUTATED 20P LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO                4                618
[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 644 226
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 6                870 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 2                226 
$`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-8328 TCGA-KL-8339 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 
      102.81        28.11        23.28        28.80        47.24       130.13 
TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 
       47.21        38.47        34.29        31.07        42.97        82.32 
TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4707 TCGA-B0-4712 
      109.91        58.49        28.73        22.45        19.73        43.96 
TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       52.21        18.51       112.80       133.94        15.78        70.68 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 
      108.56        53.26       118.85        75.58       103.43        46.16 
TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        0.59       107.54         5.46        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-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ 
       81.21        70.13        23.01        75.42        34.85        39.88 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV 
       33.07        25.58        16.18        22.49        12.26        67.17 
TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-A4-A5Y1 TCGA-AL-3468 TCGA-AL-A5DJ 
       61.05        21.37         0.89        12.99        76.64        49.25 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A44B 
       21.67        27.68        21.07        10.16        21.86        11.87 
TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       19.23        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 
        3.02        61.02        17.95        84.89        67.17        16.34 
TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO 
       12.13        29.26        19.73        17.75        41.33        62.83 
TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8323 
       86.37        21.60        15.91        15.62         6.74        38.07 
TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8330 
      153.73        23.84       109.22       137.06        90.48       108.62 
TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8337 TCGA-KL-8340 
       98.96        84.89        98.33        96.95        44.84        66.54 
TCGA-KL-8341 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8345 TCGA-KL-8346 
       24.79        73.91        71.41        28.80        54.74        62.37 
TCGA-KM-8438 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
      151.96        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8423 TCGA-KN-8424 
      129.37        23.47        87.91        25.48        25.91        65.19 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 
      104.52         3.55         0.99        52.27        87.12        19.33 
TCGA-KN-8432 TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        2.50        11.21        59.08       115.00        42.35       100.87 
TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      105.47        10.68       100.47       103.40        92.71        16.67 
TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 
      104.55       103.10        99.88       105.60        96.62        90.48 
TCGA-KO-8417 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 
       92.55        12.66        11.90        36.82         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 
       36.36        38.99        37.38        48.82        62.01         4.50 
TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 
       52.93        45.53        29.92        18.44        88.37        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-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A6NN 
       65.52        20.28        33.47        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       117.80       122.56 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
      109.41        15.78        73.68       112.08        68.61       109.51 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
       94.19        46.78        48.36        78.64        40.01        94.29 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
       83.21        37.58        38.40        82.45        72.89        12.13 
TCGA-AS-3777 TCGA-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-B0-4710 TCGA-B0-4713 TCGA-B0-4714 
        7.82         5.98         2.14        57.70         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 
       58.45        15.72        46.59         0.59         5.52        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 
       10.29        65.29        39.45        26.07        29.03         2.27 
TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 
       36.85        70.52        20.94        43.30        11.24        11.90 
TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
        7.30        25.32        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
       21.86        52.08        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        58.59        19.30        66.05        38.63 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       52.73        41.88        52.87        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       46.39        56.98        42.41       111.52       129.67        85.78 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       86.47       126.28        80.91        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
       32.61        35.90         1.68        31.96        21.30        31.30 
TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
       31.66        32.98        21.57        16.67        12.00         5.75 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
        5.10         1.25         0.53         4.64         5.46         0.36 
TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        0.23        23.31        16.80        49.97        42.71        25.05 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       45.37        17.19        25.55        50.14        40.04        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        50.14        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
       48.53         0.53        34.39        14.30        27.29        29.88 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ 
       17.06         1.74         4.93        17.36        16.27        14.17 
TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       85.51        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       54.90        97.45        53.42        27.78        62.07        37.25 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       21.21        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-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-4784 
        5.33        61.97        13.51        56.91        68.38        60.95 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 
       15.78        48.95        36.53        36.39        10.98        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 
        6.71        47.97        87.45        71.41        63.62        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       61.22         6.74        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       33.34        46.45        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        43.00        30.64        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       35.21        28.87         6.35        79.30         2.04        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
       37.25        37.22        22.78        13.35        33.24        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 
       13.41        24.62        33.47        19.82        34.95         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
      115.00        46.55        14.17       106.16       114.41        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
       58.95        11.05        21.24        83.97        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06       116.84        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83       113.46        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 
       51.52        63.98       115.69        50.01        24.66        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
      109.84        50.24        56.35        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       58.75         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       90.54        91.69        55.33        94.45        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       21.76        69.96        84.30        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX TCGA-DV-A4VZ TCGA-EU-5904 
       14.63        22.78        62.63        53.46        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE 
        2.01        19.43        19.96        16.37        11.70         7.04 
TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 
       75.55        59.01        58.22       100.27        56.91         4.57 
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JM 
       91.73        56.81        54.64        51.52        38.99        30.71 
TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93X 
       24.33        31.20        29.36         5.29         0.13        12.82 
TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
       11.57       106.55        49.58        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 TCGA-5P-A9KA 
       15.48        71.80        62.93        43.04        19.36        12.99 
TCGA-5P-A9KC TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 
       12.39        27.09        67.43        18.21        19.63         0.10 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       35.18        19.13         7.82         0.23        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
       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        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       37.51        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 
       29.03        30.58        34.49        12.46        50.50        28.18 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 
       26.40        20.61         0.46         1.15        43.99        22.06 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       17.23         0.16        14.86        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
       19.27         8.88        63.72        22.92        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5889 
       21.63        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
        7.17         3.81        40.77        79.86        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       74.60        34.19        19.00        24.89        10.68        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
        2.40         1.18         0.43         4.01        51.78        90.90 
TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
       11.05        39.25        71.44        25.15        20.52        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
       25.25        17.98        23.08        16.90        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI 
       11.21        16.31        81.93        58.19        26.01        11.84 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       56.75        73.25        25.22        16.80        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 
       85.78        88.24        96.69        22.26        21.34        12.36 
TCGA-J7-6720 TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
       12.76        10.55        10.09        18.41        29.10        11.41 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
       34.29        27.78        30.38        27.65        20.25        17.62 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       31.13        15.48        99.78        87.09        42.94         6.61 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO 
       99.12        92.58        52.27        16.01        50.60        78.90 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
       14.07        47.90        49.45        44.61        28.80        27.06 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       11.93        19.00        16.31        41.62        26.47        53.10 
TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       43.76        18.02        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
       37.35        98.96        86.27        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  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 
            65.950             35.885 
[1] "18.5 - 92.5 (66.0)" "0.1 - 194.8 (35.9)"
[1] "hr=" "1.1"
D78V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  20Q LOSS MUTATED         1        1         2        2
  20Q LOSS WILD-TYPE     453      102       188      102
D78V3, multiclass
           clus
vv          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  STAGE I                  1                453
  STAGE II                 1                102
  STAGE III                2                188
  STAGE IV                 2                102
[1] 4 2
[1] TRUE
[1] "dimension of 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 479 125 255  15
D78V4, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  T1                1                479
  T2                2                125
  T3                3                255
  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 321  44   5
D78V5, multiclass
    clus
vv   20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  N0                2                321
  N1                0                 44
  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 541  88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      5    1
  20Q LOSS WILD-TYPE  541   88
   clus
vv  20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  0                5                541
  1                1                 88
[1] 2 2
[1] FALSE
D78V7, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     2   4
  20Q LOSS WILD-TYPE 290 586
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      2    4
  20Q LOSS WILD-TYPE  290  586
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                2                290
  MALE                  4                586
[1] 2 2
[1] FALSE
D78V8, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     3   0
  20Q LOSS WILD-TYPE 405   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      3    0
  20Q LOSS WILD-TYPE  405    3
     clus
vv    20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  NO                 3                405
  YES                0                  3
[1] 2 2
[1] FALSE
D78V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  20Q LOSS MUTATED                    3                                 3
  20Q LOSS WILD-TYPE                 63                               525
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  20Q LOSS MUTATED                                       0
  20Q LOSS WILD-TYPE                                   288
D78V10, multiclass
                                       clus
vv                                      20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   3                 63
  KIDNEY CLEAR CELL RENAL CARCINOMA                    3                525
  KIDNEY PAPILLARY RENAL CELL CARCINOMA                0                288
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                105 
        TCGA-B8-4621         TCGA-DV-A4W0         TCGA-G6-A8L7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-2Z-A9JQ         TCGA-5P-A9JU 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B9-A44B         TCGA-DW-5561         TCGA-DW-7834 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DW-7838         TCGA-GL-A59T         TCGA-IZ-A6M8 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-PJ-A5Z9         TCGA-UZ-A9PO         TCGA-UZ-A9PR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RZ         TCGA-KL-8324         TCGA-KL-8330 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KL-8341         TCGA-KL-8345         TCGA-KM-8639 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KN-8428         TCGA-KN-8433         TCGA-KO-8408 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-KO-8409         TCGA-KO-8416         TCGA-A3-A8CQ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A3-A8OV         TCGA-A3-A8OW         TCGA-AK-3445 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AK-3451         TCGA-B2-A4SR         TCGA-B8-4146 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5164         TCGA-B8-5550 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B8-A54E         TCGA-B8-A54F         TCGA-B8-A54G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B8-A8YJ         TCGA-DV-A4VX         TCGA-G6-A5PC 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MM-A563         TCGA-T7-A92I         TCGA-2Z-A9J2 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J5         TCGA-2Z-A9J7         TCGA-2Z-A9J8 
"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-4A-A93W 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-4A-A93Y         TCGA-5P-A9K3         TCGA-5P-A9KE 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A4-8310         TCGA-A4-A48D         TCGA-A4-A57E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-A4-A5Y0         TCGA-AL-3466         TCGA-AL-3472 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-AL-7173         TCGA-B1-A654         TCGA-B9-4114 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B9-4115         TCGA-B9-4117         TCGA-B9-7268 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B9-A69E         TCGA-DW-7963         TCGA-F9-A97G 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G7-6792         TCGA-G7-6793         TCGA-G7-6795 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G7-7501         TCGA-G7-A8LB         TCGA-G7-A8LD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G7-A8LE         TCGA-GL-7773         TCGA-GL-A9DD 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-HE-A5NI         TCGA-HE-A5NJ         TCGA-HE-A5NK 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-IA-A40U         TCGA-IA-A83S         TCGA-IA-A83V 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P4-A5EB         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-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Y8-A894         TCGA-Y8-A896         TCGA-Y8-A8RY 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
D78V12, continuous
[1] "Remove cluster labels:" "20Q LOSS MUTATED"      
clus
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 1                 73 
        TCGA-DV-A4W0         TCGA-G6-A8L7         TCGA-MM-A84U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9JD         TCGA-DW-5561         TCGA-PJ-A5Z9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-UZ-A9PO         TCGA-UZ-A9PR         TCGA-Y8-A8RZ 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        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-AK-3445         TCGA-AK-3451         TCGA-B2-A4SR 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-B8-5158         TCGA-B8-5550         TCGA-MM-A563 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-T7-A92I         TCGA-2Z-A9J3         TCGA-2Z-A9J7 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-2Z-A9J8         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-B9-4114         TCGA-B9-4117         TCGA-B9-A69E 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-DW-7963         TCGA-F9-A97G         TCGA-G7-6793 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-G7-6795         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-A9DD         TCGA-HE-A5NI         TCGA-IA-A40U 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-MH-A854         TCGA-MH-A856         TCGA-P4-A5E6 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-P4-AAVK         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-A9PS         TCGA-UZ-A9PX         TCGA-WN-A9G9 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-WN-AB4C         TCGA-Y8-A894         TCGA-Y8-A896 
"20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" "20Q LOSS WILD-TYPE" 
        TCGA-Y8-A8RY 
"20Q LOSS WILD-TYPE" 
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  20Q LOSS MUTATED                                  0     0
  20Q LOSS WILD-TYPE                                2    16
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED                           0     6
  20Q LOSS WILD-TYPE                       121   713
D78V13, multiclass
                                  clus
vv                                 20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           0                 16
  BLACK OR AFRICAN AMERICAN                       0                121
  WHITE                                           6                713
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V14, binary
                    cls
clus                   0   1
  20Q LOSS MUTATED     1   0
  20Q LOSS WILD-TYPE  41 622
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      1    0
  20Q LOSS WILD-TYPE   41  622
                        clus
vv                       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    1                 41
  NOT HISPANIC OR LATINO                0                622
[1] 2 2
[1] FALSE

Clustering(79) Variable = 21Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                  0   1
  21Q LOSS MUTATED    95  36
  21Q LOSS WILD-TYPE 553 192
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
               131                745 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                36                192 
$`21Q LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KO-8411 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-5695 
      102.81        28.11       130.13        19.73        43.96        70.68 
TCGA-CJ-5689 TCGA-2Z-A9JT TCGA-A4-7288 TCGA-AL-3468 TCGA-B9-A44B TCGA-B9-A5W7 
       53.26        22.49        61.05        76.64        11.87        19.23 
TCGA-DZ-6134 TCGA-HE-A5NF TCGA-PJ-A5Z9 TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 
       61.02        84.89        17.75        38.07       153.73        23.84 
TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8334 TCGA-KL-8336 TCGA-KL-8338 
      108.62        98.96        84.89        96.95        30.25        86.56 
TCGA-KL-8340 TCGA-KL-8341 TCGA-KL-8343 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8443 
       66.54        24.79        71.41        28.80        62.37        49.97 
TCGA-KM-8476 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8425 TCGA-KN-8427 TCGA-KN-8428 
      123.12        25.48        65.19       104.52         0.99        52.27 
TCGA-KN-8429 TCGA-KN-8432 TCGA-KN-8434 TCGA-KO-8403 TCGA-KO-8406 TCGA-KO-8408 
       87.12         2.50        59.08       105.47       103.40        16.67 
TCGA-KO-8409 TCGA-KO-8414 TCGA-KO-8415 TCGA-KO-8416 TCGA-A3-3317 TCGA-A3-3374 
      104.55       105.60        96.62        90.48        49.02        43.20 
TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3465 TCGA-AS-3777 
      117.80        15.78       112.08        94.19        12.13        40.70 
TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4811 TCGA-B0-4828 TCGA-B0-4834 
        1.38         3.62        57.70        46.59        10.09        68.71 
TCGA-B0-5084 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5697 TCGA-B4-5838 TCGA-B8-4619 
        7.30        52.87        42.41        86.47         5.46        17.19 
TCGA-B8-5553 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4340 TCGA-BP-4768 
       14.30        62.24        97.45        21.21        18.48        13.15 
TCGA-BP-4770 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4994 TCGA-BP-5169 
       10.82         6.71        71.41        46.45        43.00         6.35 
TCGA-BP-5198 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4907 
       19.82        66.21       109.84        47.67        51.29        49.28 
TCGA-CJ-4913 TCGA-CJ-4923 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CW-5588 TCGA-CW-6087 
       38.56        18.81        67.00        53.42        66.31         1.35 
TCGA-CZ-4860 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-DV-A4VX 
        6.77        90.54        91.69        84.30        22.52        53.46 
TCGA-MM-A563 TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-2Z-A9JM TCGA-4A-A93X TCGA-5P-A9JY 
       19.43        56.91        51.52        30.71        12.82        49.58 
TCGA-5P-A9K9 TCGA-A4-8516 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       19.36         0.76        16.96         8.48        16.31        15.75 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-4114 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5885 
       33.83        29.03        28.18        17.23        86.76        30.28 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7061 TCGA-F9-A4JJ TCGA-F9-A7Q0 
       10.82         7.66         2.76         7.17        10.68        13.08 
TCGA-G7-6789 TCGA-G7-6796 TCGA-GL-7966 TCGA-GL-A9DC TCGA-HE-7130 TCGA-IA-A40U 
        4.01        71.44         3.68        12.89        58.19        16.80 
TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-UZ-A9PN TCGA-UZ-A9PP 
        2.04        29.10        11.41        37.35        98.96 

$`21Q LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 
       23.28        28.80        47.24        47.21        38.47        34.29 
TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 
       31.07        42.97        82.32       109.91        58.49        28.73 
TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 
       22.45        52.21        18.51       112.80       133.94        15.78 
TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H 
      119.38       126.05        24.82        25.91         1.18         8.42 
TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 
       15.42       111.02        94.72        32.61         3.58        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4891 TCGA-CJ-4894 
       44.55        31.27        63.25       105.37        26.93        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
      107.54         5.46        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        81.21 
TCGA-G6-A8L7 TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL 
       70.13        23.01        75.42        34.85        39.88        33.07 
TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7584 TCGA-A4-7734 
       25.58        16.18        12.26        67.17        21.37         0.89 
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       12.99        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-5155 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 
       21.86        26.04        13.25        11.97        96.92        44.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       26.27        20.12        11.28        48.85        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
       35.93        37.55        24.46        13.78         3.75        14.63 
TCGA-DW-7842 TCGA-GL-A59T TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 
        3.02        17.95        67.17        16.34        12.13        29.26 
TCGA-PJ-A5Z8 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 
       19.73        41.33        62.83        86.37        21.60        15.91 
TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 TCGA-KL-8333 
       15.62         6.74       109.22       137.06        90.48        98.33 
TCGA-KL-8335 TCGA-KL-8337 TCGA-KL-8342 TCGA-KL-8345 TCGA-KM-8438 TCGA-KM-8440 
       92.55        44.84        73.91        54.74       151.96        44.91 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8423 
       51.06        31.33       129.37        23.47        87.91        25.91 
TCGA-KN-8426 TCGA-KN-8431 TCGA-KN-8433 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 
        3.55        19.33        11.21       115.00        42.35       100.87 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8407 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8417 
       10.68       100.47        92.71       103.10        99.88        92.55 
TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
       12.66        11.90        36.82         0.53        39.16        24.16 
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
       49.08        37.15        49.58        48.59        36.36        38.99 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       37.38        48.82        62.01         4.50        52.93        45.53 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
       29.92        18.44        88.37        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-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
       29.10       122.56       109.41        73.68        68.61       109.51 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 
       46.78        48.36        78.64        40.01        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        82.45        72.89         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-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4713 TCGA-B0-4714 
       65.10         7.82         5.98         2.14         6.64         3.25 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4816 TCGA-B0-4817 
       58.45        15.72         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-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       29.10        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        10.52        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 
        8.05         2.24        21.86        52.08        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        41.88        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 
       48.82        46.39        56.98       111.52       129.67        85.78 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
      126.28        80.91        71.41        73.84       149.16       105.37 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3923 
      130.65        79.89       131.15        89.49        91.46        32.61 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       35.90         1.68        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
        1.25         0.53         4.64         0.36         0.23        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        49.97        42.71        25.05        45.37        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       50.14        40.04        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       50.14        16.60         6.38        48.53         0.53        34.39 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J 
       27.29        29.88        17.06         1.74         4.93        17.36 
TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       16.27        14.17        85.51        90.28       101.06        93.34 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4174 
       99.85         0.43        89.36        23.05        77.03        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
       64.27        54.90        53.42        27.78        62.07        37.25 
TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4346 
       15.62         0.07        93.99        52.24        62.86        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
       48.07        61.68         5.33        61.97        13.51        56.91 
TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        60.95        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       10.98        36.95        47.97        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
       60.30        61.22         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-4977 
       48.89        49.38        45.50         6.94        47.11        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
       36.07        33.34        31.30        36.95         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
       16.47        30.64        18.51        38.70        37.02        37.48 
TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       35.21        28.87        79.30         2.04        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
       52.27         9.63        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       37.22        22.78        13.35        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       24.62        33.47        34.95         0.95       115.00        46.55 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17       106.16       114.41        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       11.05        21.24        83.97        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
       74.27        75.06       116.84        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       113.46        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 
      115.69        50.01        24.66        39.45        50.24        56.35 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 
       49.97        49.18        50.33        54.48        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
        4.57       131.08        72.00       129.40       133.71        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15       122.83        62.10 
TCGA-CJ-5684 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       73.35        62.66       119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
      105.93        83.90        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
       58.75        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5459 
       58.82        79.53        23.74        18.44        79.63        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5467 
       94.45        10.85        10.22        21.76        69.96         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-A4VZ TCGA-EU-5904 
       12.26        14.63        22.78        62.63        12.00        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L8 
        3.91         6.77         4.18         7.96        10.29        35.87 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
        2.01        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9JE 
       59.01        58.22       100.27         4.57        91.73        56.81 
TCGA-2Z-A9JG TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       54.64        38.99        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 TCGA-5P-A9K2 
        0.13        11.57       106.55        90.21        22.26        78.64 
TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9KA TCGA-5P-A9KC 
       15.48        71.80        62.93        43.04        12.99        12.39 
TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       27.09        67.43        18.21        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
       19.13         7.82         0.23        16.64        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8518 
       25.64        23.97        23.28        23.31        19.63        19.73 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3466 TCGA-AL-3467 
       14.33        12.46         8.28        12.46         9.63        70.19 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 
       49.32        66.71        62.66        67.73         2.20        41.13 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 
       37.51        36.49        20.25        16.77        20.32        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
       34.49        12.46        50.50        26.40        20.61         0.46 
TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
        1.15        43.99        22.06         0.16        14.86        17.49 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 
       12.30        19.27         8.88        63.72        22.92        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5891 
       47.80        21.63        40.83        26.04        25.35         0.95 
TCGA-BQ-5893 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
        7.92       123.62        48.26        93.34        61.28        50.40 
TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6131 
       49.84         7.63         7.04         3.81        40.77        79.86 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
       80.88        51.19        74.60        34.19        19.00        24.89 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 
        2.40         1.18         0.43        51.78        90.90        11.05 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       39.25        25.15        20.52        25.84        25.25        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
       23.08        16.90        80.65       194.79        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH 
        1.05        12.43        11.21        16.31        81.93        26.01 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X TCGA-IA-A83S 
       11.84        56.75        73.25        25.22        19.99        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-8537 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       10.55        10.09        18.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S 
       16.01        50.60        78.90        14.07        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PJ 
       41.62        26.47        53.10        43.76        18.02        26.20 
TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-UZ-A9PU 
      117.40       103.63       125.29        86.27        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.76               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            153.73             194.79 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             42.41              34.95 
[1] "0.8 - 153.7 (42.4)" "0.1 - 194.8 (35.0)"
[1] "hr=" "1"  
D79V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  21Q LOSS MUTATED        47       20        39       22
  21Q LOSS WILD-TYPE     407       83       151       82
D79V3, multiclass
           clus
vv          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                 47                407
  STAGE II                20                 83
  STAGE III               39                151
  STAGE IV                22                 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
  21Q LOSS MUTATED    48  24  55   6
  21Q LOSS WILD-TYPE 432 103 203   9
D79V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1               48                432
  T2               24                103
  T3               55                203
  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    50  13   4
  21Q LOSS WILD-TYPE 273  31   2
D79V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               50                273
  N1               13                 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"
D79V6, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    77  12
  21Q LOSS WILD-TYPE 469  77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     77   12
  21Q LOSS WILD-TYPE  469   77
   clus
vv  21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  0               77                469
  1               12                 77
[1] 2 2
[1] FALSE
D79V7, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    48  85
  21Q LOSS WILD-TYPE 244 505
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     48   85
  21Q LOSS WILD-TYPE  244  505
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               48                244
  MALE                 85                505
[1] 2 2
[1] FALSE
D79V8, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED    78   0
  21Q LOSS WILD-TYPE 330   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     78    0
  21Q LOSS WILD-TYPE  330    3
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                78                330
  YES                0                  3
[1] 2 2
[1] FALSE
D79V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  21Q LOSS MUTATED                   35                                55
  21Q LOSS WILD-TYPE                 31                               473
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  21Q LOSS MUTATED                                      43
  21Q LOSS WILD-TYPE                                   245
D79V10, multiclass
                                       clus
vv                                      21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                  35                 31
  KIDNEY CLEAR CELL RENAL CARCINOMA                   55                473
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               43                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"
D79V11, continuous
D79V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  21Q LOSS MUTATED                                  0     3
  21Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED                          10   114
  21Q LOSS WILD-TYPE                       111   605
D79V13, multiclass
                                  clus
vv                                 21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 13
  BLACK OR AFRICAN AMERICAN                      10                111
  WHITE                                         114                605
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D79V14, binary
                    cls
clus                   0   1
  21Q LOSS MUTATED     4  88
  21Q LOSS WILD-TYPE  38 534
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      4   88
  21Q LOSS WILD-TYPE   38  534
                        clus
vv                       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  HISPANIC OR LATINO                    4                 38
  NOT HISPANIC OR LATINO               88                534
[1] 2 2
[1] FALSE

Clustering(80) Variable = 22Q LOSS MUTATION ANALYSIS
D80V1, survival
                    sevent
clus2                  0   1
  22Q LOSS MUTATED    68  38
  22Q LOSS WILD-TYPE 580 190
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
               106                770 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                38                190 
$`22Q LOSS MUTATED`
TCGA-KL-8339 TCGA-B0-4707 TCGA-B0-4712 TCGA-BP-4799 TCGA-BP-4986 TCGA-CJ-4891 
       28.11        19.73        43.96        37.25        25.81        26.93 
TCGA-CJ-5689 TCGA-DV-5566 TCGA-5P-A9JU TCGA-A4-7288 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
       53.26        45.96        12.26        61.05        12.99        49.25 
TCGA-B1-A47O TCGA-B9-A44B TCGA-BQ-7055 TCGA-BQ-7056 TCGA-Y8-A8RZ TCGA-KL-8330 
       27.68        11.87        26.27        20.12         6.74       108.62 
TCGA-KL-8331 TCGA-KL-8336 TCGA-KM-8438 TCGA-KN-8422 TCGA-KO-8415 TCGA-A3-3347 
       98.96        30.25       151.96        25.48        96.62        52.93 
TCGA-AK-3453 TCGA-AK-3456 TCGA-B0-4828 TCGA-B0-4844 TCGA-B0-5092 TCGA-B0-5094 
       83.21        37.58        10.09        10.29        15.09        10.95 
TCGA-B0-5098 TCGA-B0-5116 TCGA-B0-5701 TCGA-B2-4098 TCGA-B8-4143 TCGA-B8-A54E 
       52.08        41.88        80.91         1.68        23.31        29.88 
TCGA-BP-4343 TCGA-BP-4768 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4985 TCGA-BP-4992 
       62.86        13.15        71.41         6.74        31.30        16.47 
TCGA-BP-5175 TCGA-BP-5196 TCGA-CJ-4637 TCGA-CJ-4640 TCGA-CJ-4897 TCGA-CJ-4901 
       30.64        33.47        73.22       114.41       109.84        47.67 
TCGA-CJ-6028 TCGA-CW-6097 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5468 
       53.42        18.77       107.41        90.54        10.85         1.94 
TCGA-CZ-5469 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9JY TCGA-5P-A9KC 
       31.10        54.64        51.52        12.82        49.58        12.39 
TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-AL-3466 TCGA-B1-7332 
       18.21        29.46        19.63         8.28         9.63        37.51 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5879 
       33.83        29.03        17.23        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-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ 
       61.28        50.40         7.17        79.86        19.00        10.68 
TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6797 TCGA-G7-7501 
       13.08         1.18         4.01        11.05        25.15        20.52 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-MH-A856 
       25.84        23.08         3.68         2.04        10.55        31.13 
TCGA-P4-A5EA TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-SX-A7SM TCGA-UN-AAZ9 
        6.61        78.90        14.07        27.06        11.93        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A896 
       37.35        86.27        39.06        18.64 

$`22Q LOSS WILD-TYPE`
TCGA-KL-8328 TCGA-KM-8439 TCGA-KM-8441 TCGA-KM-8442 TCGA-KO-8411 TCGA-A3-3307 
      102.81        23.28        28.80        47.24       130.13        47.21 
TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 
       38.47        34.29        31.07        42.97        82.32       109.91 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 
       58.49        28.73        22.45        52.21        18.51       112.80 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 
      133.94        15.78        70.68       119.38       126.05        24.82 
TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 
       25.91         1.18         8.42        15.42       111.02        94.72 
TCGA-BP-4164 TCGA-BP-4327 TCGA-BP-4331 TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 
       32.61         3.58        80.68        74.17        54.77        12.33 
TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 
       77.62        44.15        60.59        11.64        20.38         6.94 
TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       61.51        53.65        27.22         5.82        45.07        41.62 
TCGA-BP-5006 TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 
       27.62        35.90        48.10        62.86        49.15        27.02 
TCGA-BP-5191 TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4894 
       31.79        44.55        31.27        63.25       105.37        27.65 
TCGA-CJ-4904 TCGA-CJ-6027 TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 
      108.56       118.85        75.58       103.43        46.16         0.59 
TCGA-CZ-4862 TCGA-CZ-4865 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
      107.54         5.46        43.69        65.88        12.16        11.67 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-DV-A4W0 TCGA-G6-A8L7 
       37.15        66.28        56.84        23.90        81.21        70.13 
TCGA-MM-A84U TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ 
       23.01        75.42        34.85        39.88        33.07        25.58 
TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-5P-A9JV TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       16.18        22.49        67.17        21.37         0.89        76.64 
TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-A5W7 TCGA-BQ-5886 
       21.67        21.07        10.16        21.86        19.23        26.04 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7058 TCGA-DW-5560 
       13.25        11.97        96.92        44.84        11.28        48.85 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
       13.61       129.86        35.93        37.55        24.46        13.78 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF 
        3.75        14.63         3.02        61.02        17.95        84.89 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
       67.17        16.34        12.13        29.26        19.73        17.75 
TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 
       41.33        62.83        86.37        21.60        15.91        15.62 
TCGA-KL-8323 TCGA-KL-8324 TCGA-KL-8325 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8329 
       38.07       153.73        23.84       109.22       137.06        90.48 
TCGA-KL-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-KL-8346 TCGA-KM-8440 TCGA-KM-8443 TCGA-KM-8476 TCGA-KM-8477 TCGA-KM-8639 
       62.37        44.91        49.97       123.12        51.06        31.33 
TCGA-KN-8418 TCGA-KN-8419 TCGA-KN-8421 TCGA-KN-8423 TCGA-KN-8424 TCGA-KN-8425 
      129.37        23.47        87.91        25.91        65.19       104.52 
TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
        3.55         0.99        52.27        87.12        19.33         2.50 
TCGA-KN-8433 TCGA-KN-8434 TCGA-KN-8435 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8403 
       11.21        59.08       115.00        42.35       100.87       105.47 
TCGA-KO-8404 TCGA-KO-8405 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8409 
       10.68       100.47       103.40        92.71        16.67       104.55 
TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-KO-8416 TCGA-KO-8417 TCGA-3Z-A93Z 
      103.10        99.88       105.60        90.48        92.55        12.66 
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
       11.90        36.82         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-A3-3346 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01         4.50        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI 
       18.64        18.87        28.31        65.52        20.28        33.47 
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-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       29.10       117.80       122.56       109.41        15.78        73.68 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
      112.08        68.61       109.51        94.19        46.78        48.36 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       78.64        40.01        94.29        38.40        82.45        72.89 
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-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        3.25        58.45        15.72        46.59         0.59         5.52 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 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        10.52 
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-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       25.32         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        58.59        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 
       66.05        38.63        52.73        52.87        51.02        38.43 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 
       48.82        46.39        56.98        42.41       111.52       129.67 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       85.78        86.47       126.28        71.41        73.84       149.16 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
      105.37       130.65        79.89       131.15        89.49        91.46 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
       32.61        35.90        31.96        21.30        31.30        31.66 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
       32.98        21.57        16.67        12.00         5.75         5.10 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
        1.25         0.53         4.64         5.46         0.36         0.23 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
       16.80        49.97        42.71        25.05        45.37        17.19 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.55        50.14        40.04        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        50.14        16.60         6.38        48.53         0.53 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
       34.39        14.30        27.29        17.06         1.74         4.93 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 
       17.36        16.27        14.17        85.51        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       93.34        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
       62.24        61.78        64.27        54.90        97.45        53.42 
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        15.62         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       93.99        18.48        52.24        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
       77.98         5.98        41.75        71.80        48.07        61.68 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        13.51        56.91        68.38 
TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       60.95        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97        87.45        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22        57.40        58.98        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 
       49.38        45.50         6.94        47.11        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4994 
       33.34        46.45        36.95         3.88        46.45        43.00 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       30.64        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5176 
       28.87         6.35        79.30         2.04        74.20        52.27 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        33.24        23.47        13.41        24.62 
TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4638 
       19.82        34.95         0.95       115.00        46.55        14.17 
TCGA-CJ-4639 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      106.16        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4902 TCGA-CJ-4903 
       24.66        39.45        50.24        56.35        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81       131.08        72.00       129.40 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
      133.71        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
      122.83        62.10        73.35        67.00        62.66       119.64 
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-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 
       83.90        25.45        47.08        69.21        58.75         6.77 
TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       14.66        63.39        93.04        63.42        58.82        79.53 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       23.74        18.44        79.63        91.69        55.33        94.45 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.22        21.76        69.96        84.30        22.52         2.40 
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-A4VX TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 
       22.78        62.63        53.46        12.00        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-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
       19.43        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9J8 
       59.01        58.22       100.27        56.91         4.57        91.73 
TCGA-2Z-A9JE TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP 
       56.81        38.99        30.71        24.33        31.20        29.36 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JZ TCGA-5P-A9K0 
        5.29         0.13        11.57       106.55        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K3 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K8 TCGA-5P-A9K9 
       78.64        15.48        71.80        62.93        43.04        19.36 
TCGA-5P-A9KA TCGA-5P-A9KE TCGA-5P-A9KH TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 
       12.99        27.09        67.43        19.63         0.10        35.18 
TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
       19.13         7.82         0.23        16.64        30.48        25.64 
TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 
       23.97        23.28        23.31         0.76        19.73        14.33 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
       12.46        16.96         8.48        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 
       41.13        36.49        20.25        16.77        20.32        30.58 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
       34.49        12.46        50.50        28.18        26.40        20.61 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-B9-A69E 
        0.46         1.15        43.99        22.06         0.16        14.86 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       17.49        12.30        19.27        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-7045 
       21.63        40.83        25.35        10.82         7.92        48.26 
TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7963 
       93.34        49.84         7.63         7.04         3.81        40.77 
TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF 
       80.88        51.19        74.60        34.19        24.89         2.40 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM 
        0.43        51.78        90.90        39.25        71.44        25.25 
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-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 
        1.05        12.43        12.89        11.21        16.31        81.93 
TCGA-HE-7130 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
       58.19        26.01        11.84        56.75        73.25        25.22 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 
       16.80        19.99        85.78        88.24        96.69        22.26 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE 
       21.34        12.36        12.76        10.09        18.41        29.10 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
       11.41        34.29        27.78        30.38        27.65        20.25 
TCGA-MH-A854 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EB 
       17.62        15.48        99.78        87.09        42.94        99.12 
TCGA-P4-A5ED TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-SX-A71R TCGA-SX-A71S 
       92.58        52.27        16.01        50.60        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
       44.61        28.80        19.00        16.31        41.62        26.47 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL TCGA-UZ-A9PM 
       53.10        43.76        26.20       117.40       103.63       125.29 
TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
       98.96        71.24        30.67        47.47        65.13       110.73 
TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A8RY 
       51.35        31.73        26.01        18.64        18.05        25.28 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
        6.02        13.28 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.95               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            151.96             194.79 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            26.600             37.185 
[1] "0.9 - 152.0 (26.6)" "0.1 - 194.8 (37.2)"
[1] "hr=" "1.8"
D80V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  22Q LOSS MUTATED        34       10        39       20
  22Q LOSS WILD-TYPE     420       93       151       84
D80V3, multiclass
           clus
vv          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                 34                420
  STAGE II                10                 93
  STAGE III               39                151
  STAGE IV                20                 84
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q LOSS MUTATED    41  14  51   1
  22Q LOSS WILD-TYPE 439 113 207  14
D80V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1               41                439
  T2               14                113
  T3               51                207
  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    33  16   3
  22Q LOSS WILD-TYPE 290  28   3
D80V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               33                290
  N1               16                 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    53  16
  22Q LOSS WILD-TYPE 493  73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     53   16
  22Q LOSS WILD-TYPE  493   73
   clus
vv  22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  0               53                493
  1               16                 73
[1] 2 2
[1] FALSE
D80V7, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    46  61
  22Q LOSS WILD-TYPE 246 529
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     46   61
  22Q LOSS WILD-TYPE  246  529
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               46                246
  MALE                 61                529
[1] 2 2
[1] FALSE
D80V8, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    51   0
  22Q LOSS WILD-TYPE 357   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     51    0
  22Q LOSS WILD-TYPE  357    3
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                51                357
  YES                0                  3
[1] 2 2
[1] FALSE
D80V9, continuous
                    vv
clus                 KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  22Q LOSS MUTATED                    8                                39
  22Q LOSS WILD-TYPE                 58                               489
                    vv
clus                 KIDNEY PAPILLARY RENAL CELL CARCINOMA
  22Q LOSS MUTATED                                      60
  22Q LOSS WILD-TYPE                                   228
D80V10, multiclass
                                       clus
vv                                      22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                   8                 58
  KIDNEY CLEAR CELL RENAL CARCINOMA                   39                489
  KIDNEY PAPILLARY RENAL CELL CARCINOMA               60                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"
D80V11, continuous
D80V12, continuous
                    vv
clus                 AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  22Q LOSS MUTATED                                  0     3
  22Q LOSS WILD-TYPE                                2    13
                    vv
clus                 BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED                          17    85
  22Q LOSS WILD-TYPE                       104   634
D80V13, multiclass
                                  clus
vv                                 22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                0                  2
  ASIAN                                           3                 13
  BLACK OR AFRICAN AMERICAN                      17                104
  WHITE                                          85                634
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D80V14, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED    10  72
  22Q LOSS WILD-TYPE  32 550
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     10   72
  22Q LOSS WILD-TYPE   32  550
                        clus
vv                       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  HISPANIC OR LATINO                   10                 32
  NOT HISPANIC OR LATINO               72                550
[1] 2 2
[1] FALSE

Clustering(81) Variable = XP LOSS MUTATION ANALYSIS
D81V1, survival
                   sevent
clus2                 0   1
  XP LOSS MUTATED    76  38
  XP LOSS WILD-TYPE 572 190
  XP LOSS MUTATED XP LOSS WILD-TYPE 
              114               762 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
               38               190 
$`XP LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-4164 TCGA-BP-4327 
      102.81        28.11        47.24       130.13        32.61         3.58 
TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-6027 TCGA-MM-A84U TCGA-A4-A5Y1 TCGA-B9-5155 
      105.37        27.65       118.85        23.01        12.99        21.86 
TCGA-B9-A44B TCGA-KL-8323 TCGA-KL-8325 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 
       11.87        38.07        23.84        90.48       108.62        98.96 
TCGA-KL-8332 TCGA-KL-8333 TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 
       84.89        98.33        96.95        92.55        30.25        44.84 
TCGA-KL-8338 TCGA-KL-8340 TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KM-8440 
       86.56        66.54        73.91        71.41        54.74        44.91 
TCGA-KM-8476 TCGA-KN-8418 TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8429 
      123.12       129.37        87.91        25.48        65.19        87.12 
TCGA-KN-8431 TCGA-KN-8432 TCGA-KN-8434 TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8406 
       19.33         2.50        59.08       115.00       105.47       103.40 
TCGA-KO-8407 TCGA-KO-8408 TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 
       92.71        16.67        96.62        90.48        92.55        36.82 
TCGA-A3-3319 TCGA-A3-3383 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
       37.15        28.31        94.19        40.01        12.13        40.70 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4845 
       28.47         3.62         0.59        68.71        40.70        65.29 
TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 
        7.30        52.08        52.87        42.41       149.16        32.61 
TCGA-B8-5159 TCGA-B8-5549 TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4959 TCGA-BP-5004 
       23.74         6.38        21.21         5.98        87.45        37.02 
TCGA-BP-5176 TCGA-BP-5180 TCGA-BP-5196 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CW-6090 
       52.27        74.40        33.47        25.71        25.25        83.90 
TCGA-CZ-5458 TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 
       91.69        84.30        65.65        14.63         4.18        35.87 
TCGA-MM-A563 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 
       19.43        91.73        54.64        51.52        12.82        15.48 
TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B1-7332 
       43.04        67.43        18.21        19.63         9.63        37.51 
TCGA-B3-3926 TCGA-B9-4116 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 
       29.03        20.61        19.27         8.88        22.92        21.63 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6793 TCGA-G7-7501 
       79.86        10.68        13.08         0.43        11.05        20.52 
TCGA-G7-A8LD TCGA-HE-7130 TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       16.90        58.19        10.55        14.07        18.02        86.27 

$`XP LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 
        1.18         8.42        15.42       111.02        94.72        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4904 TCGA-CJ-5689 
       44.55        31.27        63.25        26.93       108.56        53.26 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-2Z-A9J9 
       66.28        56.84        23.90        81.21        70.13        75.42 
TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS TCGA-2Z-A9JT 
       34.85        39.88        33.07        25.58        16.18        22.49 
TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 TCGA-AL-3468 
       12.26        67.17        61.05        21.37         0.89        76.64 
TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-A5W7 
       49.25        21.67        27.68        21.07        10.16        19.23 
TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7049 TCGA-BQ-7055 
       26.04        13.25        11.97        96.92        44.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
       20.12        11.28        48.85        13.61       129.86        35.93 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
       37.55        24.46        13.78         3.75        14.63         3.02 
TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-MH-A855 
       61.02        17.95        84.89        67.17        16.34        12.13 
TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO TCGA-UZ-A9PO TCGA-UZ-A9PR 
       29.26        19.73        17.75        41.33        62.83        86.37 
TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-KL-8324 TCGA-KL-8326 
       21.60        15.91        15.62         6.74       153.73       109.22 
TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 TCGA-KM-8438 TCGA-KM-8443 
      137.06        24.79        28.80        62.37       151.96        49.97 
TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 TCGA-KN-8425 TCGA-KN-8426 
       51.06        31.33        23.47        25.91       104.52         3.55 
TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8404 
        0.99        52.27        11.21        42.35       100.87        10.68 
TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 TCGA-KO-8414 TCGA-3Z-A93Z 
      100.47       104.55       103.10        99.88       105.60        12.66 
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
       11.90         0.53        39.16        24.16        49.08        49.02 
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-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 
       62.01         4.50        52.93        45.53        29.92        18.44 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       88.37        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-A3-3385 TCGA-A3-3387 TCGA-A3-A6NI TCGA-A3-A6NJ TCGA-A3-A6NL 
       18.87        65.52        20.28        33.47        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       117.80 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
      122.56       109.41        15.78        73.68       112.08        68.61 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 
      109.51        46.78        48.36        78.64        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        82.45        72.89         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-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72        46.59         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-B0-4837 TCGA-B0-4838 
       54.48        29.10        10.09        78.44        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        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-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        71.41        73.84       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 
       79.89       131.15        89.49        91.46        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        40.04        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 
       33.99        31.33        12.30        72.59        77.98        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-4784 TCGA-BP-4787 
       61.97        13.51        56.91        68.38        60.95        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 
       48.95        36.53        36.39        10.98        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
       47.97        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-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-4977 TCGA-BP-4981 TCGA-BP-4982 
       45.50         6.94        47.11        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       46.45        31.30        36.95         3.88        46.45        16.47 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 
       43.00        30.64        18.51        38.70        37.48        35.21 
TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       28.87         6.35        79.30         2.04        74.20        30.64 
TCGA-BP-5177 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        9.63        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 
       13.35        33.24        23.47        13.41        24.62        19.82 
TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 
       34.95         0.95       115.00        46.55        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
      106.16       114.41        54.61        58.95        11.05        21.24 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       83.97        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
      116.84        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
      113.46        64.18        30.64        51.52        63.98       115.69 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 
       50.01        24.66        39.45       109.84        50.24        56.35 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        49.97        51.29        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 
      131.08        72.00       129.40       133.71        18.87        22.32 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15       122.83        62.10        73.35        67.00        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66       119.64         7.36        64.57        92.02        81.83 
TCGA-CW-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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 
        1.35       105.93        18.77        25.45        47.08        69.21 
TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
       58.75         6.77        14.66        63.39        93.04       107.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82        79.53        23.74        18.44        79.63 
TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       90.54        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       80.19        67.96        12.26        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         3.91         6.77         7.96        10.29 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
        2.01        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       59.01        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        71.80        62.93        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       27.09         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
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-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46         1.15        43.99        22.06        17.23         0.16 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-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-5887 TCGA-BQ-5889 
       47.80        40.83        26.04        30.28        25.35        10.82 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
        7.66         0.95         7.92         2.76       123.62        48.26 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 
       93.34        61.28        50.40        49.84         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6135 
        7.17         3.81        40.77        80.88        51.19        74.60 
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        90.90        39.25        71.44        25.15        25.84 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
       25.25        17.98        23.08        80.65       194.79        12.92 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
        3.68        27.65         1.05        12.43        12.89        11.21 
TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
       16.31        81.93        26.01        11.84        56.75        73.25 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
       25.22        16.80        19.99         2.04        85.78        88.24 
TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-A8I2 
       96.69        22.26        21.34        12.36        12.76        10.09 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
       18.41        29.10        11.41        34.29        27.78        30.38 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
       27.65        20.25        17.62        31.13        15.48        99.78 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-P4-AAVK 
       87.09        42.94         6.61        99.12        92.58        52.27 
TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
       16.01        50.60        78.90        47.90        49.45        44.61 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SQ 
       28.80        27.06        11.93        19.00        16.31        41.62 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK TCGA-UZ-A9PL 
       26.47        53.10        43.76        26.20       117.40       103.63 
TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV 
      125.29        37.35        98.96        71.24        30.67        47.47 
TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 TCGA-WN-AB4C 
       65.13       110.73        51.35        31.73        26.01        39.06 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
       18.64        18.64        18.05        25.28         6.02        13.28 

  XP LOSS MUTATED XP LOSS WILD-TYPE 
             0.43              0.07 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
           149.16            194.79 
  XP LOSS MUTATED XP LOSS WILD-TYPE 
            39.04             34.67 
[1] "0.4 - 149.2 (39.0)" "0.1 - 194.8 (34.7)"
[1] "hr=" "1.1"
D81V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XP LOSS MUTATED        38       22        34       14
  XP LOSS WILD-TYPE     416       81       156       90
D81V3, multiclass
           clus
vv          XP LOSS MUTATED XP LOSS WILD-TYPE
  STAGE I                38               416
  STAGE II               22                81
  STAGE III              34               156
  STAGE IV               14                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
  XP LOSS MUTATED    40  25  47   2
  XP LOSS WILD-TYPE 440 102 211  13
D81V4, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  T1              40               440
  T2              25               102
  T3              47               211
  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    39  13   2
  XP LOSS WILD-TYPE 284  31   4
D81V5, multiclass
    clus
vv   XP LOSS MUTATED XP LOSS WILD-TYPE
  N0              39               284
  N1              13                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    65  10
  XP LOSS WILD-TYPE 481  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     65   10
  XP LOSS WILD-TYPE  481   79
   clus
vv  XP LOSS MUTATED XP LOSS WILD-TYPE
  0              65               481
  1              10                79
[1] 2 2
[1] FALSE
D81V7, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    45  69
  XP LOSS WILD-TYPE 247 521
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     45   69
  XP LOSS WILD-TYPE  247  521
        clus
vv       XP LOSS MUTATED XP LOSS WILD-TYPE
  FEMALE              45               247
  MALE                69               521
[1] 2 2
[1] FALSE
D81V8, binary
                   cls
clus                  0   1
  XP LOSS MUTATED    72   0
  XP LOSS WILD-TYPE 336   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED     72    0
  XP LOSS WILD-TYPE  336    3
     clus
vv    XP LOSS MUTATED XP LOSS WILD-TYPE
  NO               72               336
  YES               0                 3
[1] 2 2
[1] FALSE
D81V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XP LOSS MUTATED                   38                                44
  XP LOSS WILD-TYPE                 28                               484
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XP LOSS MUTATED                                      32
  XP LOSS WILD-TYPE                                   256
D81V10, multiclass
                                       clus
vv                                      XP LOSS MUTATED XP LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 38                28
  KIDNEY CLEAR CELL RENAL CARCINOMA                  44               484
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              32               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"
D81V11, continuous
D81V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XP LOSS MUTATED                                  0     4
  XP LOSS WILD-TYPE                                2    12
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XP LOSS MUTATED                          17    88
  XP LOSS WILD-TYPE                       104   631
D81V13, multiclass
                                  clus
vv                                 XP LOSS MUTATED XP LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          4                12
  BLACK OR AFRICAN AMERICAN                     17               104
  WHITE                                         88               631
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D81V14, binary
                   cls
clus                  0   1
  XP LOSS MUTATED     2  71
  XP LOSS WILD-TYPE  40 551
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XP LOSS MUTATED      2   71
  XP LOSS WILD-TYPE   40  551
                        clus
vv                       XP LOSS MUTATED XP LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              71               551
[1] 2 2
[1] FALSE

Clustering(82) Variable = XQ LOSS MUTATION ANALYSIS
D82V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    73  40
  XQ LOSS WILD-TYPE 575 188
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
              113               763 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               40               188 
$`XQ LOSS MUTATED`
TCGA-KL-8328 TCGA-KL-8339 TCGA-KM-8442 TCGA-KO-8411 TCGA-BP-4164 TCGA-BP-4327 
      102.81        28.11        47.24       130.13        32.61         3.58 
TCGA-CJ-4642 TCGA-CJ-4894 TCGA-CJ-6027 TCGA-A4-A5Y1 TCGA-B9-5155 TCGA-KL-8323 
      105.37        27.65       118.85        12.99        21.86        38.07 
TCGA-KL-8325 TCGA-KL-8329 TCGA-KL-8330 TCGA-KL-8331 TCGA-KL-8332 TCGA-KL-8333 
       23.84        90.48       108.62        98.96        84.89        98.33 
TCGA-KL-8334 TCGA-KL-8335 TCGA-KL-8336 TCGA-KL-8337 TCGA-KL-8338 TCGA-KL-8340 
       96.95        92.55        30.25        44.84        86.56        66.54 
TCGA-KL-8342 TCGA-KL-8343 TCGA-KL-8345 TCGA-KM-8440 TCGA-KM-8476 TCGA-KN-8418 
       73.91        71.41        54.74        44.91       123.12       129.37 
TCGA-KN-8421 TCGA-KN-8422 TCGA-KN-8424 TCGA-KN-8429 TCGA-KN-8431 TCGA-KN-8432 
       87.91        25.48        65.19        87.12        19.33         2.50 
TCGA-KN-8435 TCGA-KO-8403 TCGA-KO-8404 TCGA-KO-8406 TCGA-KO-8407 TCGA-KO-8408 
      115.00       105.47        10.68       103.40        92.71        16.67 
TCGA-KO-8415 TCGA-KO-8416 TCGA-KO-8417 TCGA-A3-3306 TCGA-A3-3319 TCGA-A3-3346 
       96.62        90.48        92.55        36.82        37.15         4.50 
TCGA-A3-3382 TCGA-AK-3440 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 
       18.87        94.19        78.64        40.01        12.13        40.70 
TCGA-B0-4696 TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4845 
       28.47         3.62         0.59        68.71        40.70        65.29 
TCGA-B0-5084 TCGA-B0-5098 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5705 TCGA-B2-3923 
        7.30        52.08        52.87        42.41       149.16        32.61 
TCGA-B8-5159 TCGA-B8-5549 TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4770 
       23.74         6.38        21.21        12.30         5.98        10.82 
TCGA-BP-4959 TCGA-BP-5004 TCGA-BP-5180 TCGA-BP-5196 TCGA-CJ-5677 TCGA-CJ-5680 
       87.45        37.02        74.40        33.47        25.71        25.25 
TCGA-CW-6090 TCGA-CZ-5465 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 TCGA-G6-A8L8 
       83.90        84.30        65.65        14.63         4.18        35.87 
TCGA-MM-A563 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-4A-A93X TCGA-5P-A9K3 
       19.43        91.73        54.64        51.52        12.82        15.48 
TCGA-5P-A9K8 TCGA-5P-A9KH TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-3466 TCGA-B1-7332 
       43.04        67.43        18.21        19.63         9.63        37.51 
TCGA-B3-3926 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5882 TCGA-DZ-6131 
       29.03        19.27         8.88        22.92        21.63        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        20.52        16.90 
TCGA-HE-7130 TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-UN-AAZ9 TCGA-UZ-A9PQ 
       58.19        10.55        14.07        18.02        86.27 

$`XQ LOSS WILD-TYPE`
TCGA-KM-8439 TCGA-KM-8441 TCGA-A3-3307 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3343 
       23.28        28.80        47.21        38.47        34.29        31.07 
TCGA-A3-3358 TCGA-A3-3359 TCGA-AK-3425 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 
       42.97        82.32       109.91        58.49        28.73        22.45 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4815 TCGA-B0-5088 TCGA-B0-5691 TCGA-B0-5693 
       19.73        43.96        52.21        18.51       112.80       133.94 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5812 TCGA-B2-5635 TCGA-B8-4621 
       15.78        70.68       119.38       126.05        24.82        25.91 
TCGA-B8-5162 TCGA-B8-A54H TCGA-B8-A54K TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4331 
        1.18         8.42        15.42       111.02        94.72        80.68 
TCGA-BP-4342 TCGA-BP-4344 TCGA-BP-4353 TCGA-BP-4760 TCGA-BP-4762 TCGA-BP-4775 
       74.17        54.77        12.33        77.62        44.15        60.59 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4799 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 
       11.64        20.38        37.25         6.94        61.51        53.65 
TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5006 
       25.81        27.22         5.82        45.07        41.62        27.62 
TCGA-BP-5009 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5181 TCGA-BP-5189 TCGA-BP-5191 
       35.90        48.10        62.86        49.15        27.02        31.79 
TCGA-BP-5199 TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4891 TCGA-CJ-4904 TCGA-CJ-5689 
       44.55        31.27        63.25        26.93       108.56        53.26 
TCGA-CJ-6030 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4865 
       75.58       103.43        46.16         0.59       107.54         5.46 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-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-G6-A8L7 TCGA-MM-A84U 
       66.28        56.84        23.90        81.21        70.13        23.01 
TCGA-2Z-A9J9 TCGA-2Z-A9JD TCGA-2Z-A9JJ TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-2Z-A9JS 
       75.42        34.85        39.88        33.07        25.58        16.18 
TCGA-2Z-A9JT TCGA-5P-A9JU TCGA-5P-A9JV TCGA-A4-7288 TCGA-A4-7584 TCGA-A4-7734 
       22.49        12.26        67.17        61.05        21.37         0.89 
TCGA-AL-3468 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-A6W5 
       76.64        49.25        21.67        27.68        21.07        10.16 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
       11.87        19.23        26.04        13.25        11.97        96.92 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-DW-5560 TCGA-DW-5561 
       44.84        26.27        20.12        11.28        48.85        13.61 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
      129.86        35.93        37.55        24.46        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6134 TCGA-GL-A59T TCGA-HE-A5NF TCGA-IA-A83W 
       14.63         3.02        61.02        17.95        84.89        67.17 
TCGA-IZ-A6M8 TCGA-MH-A855 TCGA-MH-A857 TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A7SO 
       16.34        12.13        29.26        19.73        17.75        41.33 
TCGA-UZ-A9PO TCGA-UZ-A9PR TCGA-UZ-A9PZ TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RZ 
       62.83        86.37        21.60        15.91        15.62         6.74 
TCGA-KL-8324 TCGA-KL-8326 TCGA-KL-8327 TCGA-KL-8341 TCGA-KL-8344 TCGA-KL-8346 
      153.73       109.22       137.06        24.79        28.80        62.37 
TCGA-KM-8438 TCGA-KM-8443 TCGA-KM-8477 TCGA-KM-8639 TCGA-KN-8419 TCGA-KN-8423 
      151.96        49.97        51.06        31.33        23.47        25.91 
TCGA-KN-8425 TCGA-KN-8426 TCGA-KN-8427 TCGA-KN-8428 TCGA-KN-8433 TCGA-KN-8434 
      104.52         3.55         0.99        52.27        11.21        59.08 
TCGA-KN-8436 TCGA-KN-8437 TCGA-KO-8405 TCGA-KO-8409 TCGA-KO-8410 TCGA-KO-8413 
       42.35       100.87       100.47       104.55       103.10        99.88 
TCGA-KO-8414 TCGA-3Z-A93Z TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
      105.60        12.66        11.90         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-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
       37.38        48.82        62.01        52.93        45.53        29.92 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       18.44        88.37        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-A6NI TCGA-A3-A6NJ 
       18.64        28.31        65.52        20.28        33.47        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-3430 TCGA-AK-3431 TCGA-AK-3433 
      117.80       122.56       109.41        15.78        73.68       112.08 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3451 TCGA-AK-3453 
       68.61       109.51        46.78        48.36        94.29        83.21 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4688 
       37.58        38.40        82.45        72.89         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-B0-4710 TCGA-B0-4713 
       65.10         7.82         5.98         2.14        57.70         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4816 
        3.25        58.45        15.72        46.59         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-B0-4837 TCGA-B0-4838 
       54.48        29.10        10.09        78.44        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 
       53.88         6.71        56.68        10.52        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-B0-5085 TCGA-B0-5092 TCGA-B0-5094 
       43.30        11.24        11.90        25.32        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        58.59        19.30        66.05 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       38.63        52.73        41.88        51.02        38.43        48.82 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
       46.39        56.98       111.52       129.67        85.78        86.47 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
      126.28        80.91        71.41        73.84       105.37       130.65 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4098 
       79.89       131.15        89.49        91.46        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
       31.96        21.30        31.30        31.66        32.98        21.57 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
       16.67        12.00         5.75         5.10         1.25         0.53 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 
        4.64         5.46         0.36         0.23        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
       49.97        42.71        25.05        45.37        17.19        25.55 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       50.14        40.04        27.02         0.85        24.23        50.14 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
       16.60        48.53         0.53        34.39        14.30        27.29 
TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
       29.88        17.06         1.74         4.93        17.36        16.27 
TCGA-B8-A8YJ TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
       14.17        85.51        90.28       101.06        93.34        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       64.27        54.90        97.45        53.42        27.78        62.07 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       37.25        15.62         0.07        93.99        18.48        52.24 
TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       62.86        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4763 TCGA-BP-4765 
       33.99        31.33        72.59        77.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4776 
       48.07        13.15        61.68         5.33        61.97        13.51 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        60.95        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4960 
       36.39        10.98        36.95         6.71        47.97        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-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         6.94 
TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       47.11        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4998 
       36.95         3.88        46.45        16.47        43.00        30.64 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5010 TCGA-BP-5169 
       18.51        38.70        37.48        35.21        28.87         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         2.04        74.20        30.64        52.27         9.63 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5200 
       33.24        23.47        13.41        24.62        19.82        34.95 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
        0.95       115.00        46.55        73.22        14.17       106.16 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
      114.41        54.61        58.95        11.05        21.24        83.97 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06       116.84 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83       113.46 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
       64.18        30.64        51.52        63.98       115.69        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 
       24.66        39.45       109.84        50.24        56.35        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81       131.08 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 
       72.00       129.40       133.71        18.87        22.32        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 TCGA-CJ-6031 
      122.83        62.10        73.35        67.00        53.42        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 
      119.64         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-6097 TCGA-CZ-4853 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
      105.93        18.77        25.45        47.08        69.21        58.75 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        6.77        14.66        63.39        93.04       107.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82        79.53        23.74        18.44        79.63        90.54 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       91.69        55.33        94.45        10.85        10.22        21.76 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       69.96        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-A4VX 
       80.19        67.96        12.26        22.78        62.63        53.46 
TCGA-DV-A4VZ TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-G6-A5PC TCGA-G6-A8L6 
       12.00        18.12         3.91         6.77         7.96        10.29 
TCGA-GK-A6C7 TCGA-MM-A564 TCGA-MW-A4EC TCGA-T7-A92I TCGA-2K-A9WE TCGA-2Z-A9J1 
        2.01        19.96        16.37        11.70         7.04        75.55 
TCGA-2Z-A9J2 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE 
       59.01        58.22       100.27        56.91         4.57        56.81 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JR 
       38.99        30.71        24.33        31.20        29.36         5.29 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-5P-A9JW TCGA-5P-A9JY TCGA-5P-A9JZ TCGA-5P-A9K0 
        0.13        11.57       106.55        49.58        90.21        22.26 
TCGA-5P-A9K2 TCGA-5P-A9K4 TCGA-5P-A9K6 TCGA-5P-A9K9 TCGA-5P-A9KA TCGA-5P-A9KC 
       78.64        71.80        62.93        19.36        12.99        12.39 
TCGA-5P-A9KE TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7828 TCGA-A4-7915 
       27.09         0.10        35.18        19.13         7.82         0.23 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 
       16.64        30.48        29.46        25.64        23.97        23.28 
TCGA-A4-8515 TCGA-A4-8516 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-A6HP 
       16.96         8.48        16.31        15.75         8.28        12.46 
TCGA-AL-3467 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
       70.19        49.32        66.71        62.66        67.73         2.20 
TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 
       41.13        36.49        20.25        16.77        20.32        33.83 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
       30.58        34.49        12.46        50.50        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 
       20.61         0.46         1.15        43.99        22.06        17.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 
        0.16        14.86        17.49        12.30        86.76        63.72 
TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 
       43.20        47.80        40.83        26.04        30.28        25.35 
TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 
       10.82         7.66         0.95         7.92         2.76       123.62 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7059 
       48.26        93.34        61.28        50.40        49.84         7.63 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6133 
        7.04         7.17         3.81        40.77        80.88        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
       74.60        34.19        19.00        24.89         2.40         1.18 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
        4.01        51.78        90.90        39.25        71.44        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
       25.84        25.25        17.98        23.08        80.65       194.79 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
       12.92         3.68        27.65         1.05        12.43        12.89 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7129 TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       11.21        16.31        81.93        26.01        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S 
       73.25        25.22        16.80        19.99         2.04        85.78 
TCGA-IA-A83T TCGA-IA-A83V TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-J7-6720 
       88.24        96.69        22.26        21.34        12.36        12.76 
TCGA-J7-A8I2 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
       10.09        18.41        29.10        11.41        34.29        27.78 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
       30.38        27.65        20.25        17.62        31.13        15.48 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED 
       99.78        87.09        42.94         6.61        99.12        92.58 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-P4-AAVM TCGA-P4-AAVO TCGA-SX-A71R TCGA-SX-A71S 
       52.27        16.01        50.60        78.90        47.90        49.45 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SP 
       44.61        28.80        27.06        11.93        19.00        16.31 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PJ TCGA-UZ-A9PK 
       41.62        26.47        53.10        43.76        26.20       117.40 
TCGA-UZ-A9PL TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PS TCGA-UZ-A9PU 
      103.63       125.29        37.35        98.96        71.24        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-UZ-A9Q1 TCGA-V9-A7HT TCGA-WN-A9G9 
       47.47        65.13       110.73        51.35        31.73        26.01 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       39.06        18.64        18.64        18.05        25.28         6.02 
TCGA-Y8-A8S1 
       13.28 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.43              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           149.16            194.79 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            37.51             34.95 
[1] "0.4 - 149.2 (37.5)" "0.1 - 194.8 (35.0)"
[1] "hr=" "1.3"
D82V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  XQ LOSS MUTATED        38       21        33       16
  XQ LOSS WILD-TYPE     416       82       157       88
D82V3, multiclass
           clus
vv          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                38               416
  STAGE II               21                82
  STAGE III              33               157
  STAGE IV               16                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
  XQ LOSS MUTATED    40  23  46   4
  XQ LOSS WILD-TYPE 440 104 212  11
D82V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1              40               440
  T2              23               104
  T3              46               212
  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
  XQ LOSS MUTATED    41  13   2
  XQ LOSS WILD-TYPE 282  31   4
D82V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              41               282
  N1              13                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    67  10
  XQ LOSS WILD-TYPE 479  79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     67   10
  XQ LOSS WILD-TYPE  479   79
   clus
vv  XQ LOSS MUTATED XQ LOSS WILD-TYPE
  0              67               479
  1              10                79
[1] 2 2
[1] FALSE
D82V7, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    43  70
  XQ LOSS WILD-TYPE 249 520
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     43   70
  XQ LOSS WILD-TYPE  249  520
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              43               249
  MALE                70               520
[1] 2 2
[1] FALSE
D82V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    72   0
  XQ LOSS WILD-TYPE 336   3
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     72    0
  XQ LOSS WILD-TYPE  336    3
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO               72               336
  YES               0                 3
[1] 2 2
[1] FALSE
D82V9, continuous
                   vv
clus                KIDNEY CHROMOPHOBE KIDNEY CLEAR CELL RENAL CARCINOMA
  XQ LOSS MUTATED                   38                                45
  XQ LOSS WILD-TYPE                 28                               483
                   vv
clus                KIDNEY PAPILLARY RENAL CELL CARCINOMA
  XQ LOSS MUTATED                                      30
  XQ LOSS WILD-TYPE                                   258
D82V10, multiclass
                                       clus
vv                                      XQ LOSS MUTATED XQ LOSS WILD-TYPE
  KIDNEY CHROMOPHOBE                                 38                28
  KIDNEY CLEAR CELL RENAL CARCINOMA                  45               483
  KIDNEY PAPILLARY RENAL CELL CARCINOMA              30               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"
D82V11, continuous
D82V12, continuous
                   vv
clus                AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  XQ LOSS MUTATED                                  0     5
  XQ LOSS WILD-TYPE                                2    11
                   vv
clus                BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED                          14    89
  XQ LOSS WILD-TYPE                       107   630
D82V13, multiclass
                                  clus
vv                                 XQ LOSS MUTATED XQ LOSS WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE               0                 2
  ASIAN                                          5                11
  BLACK OR AFRICAN AMERICAN                     14               107
  WHITE                                         89               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"
D82V14, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     2  69
  XQ LOSS WILD-TYPE  40 553
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      2   69
  XQ LOSS WILD-TYPE   40  553
                        clus
vv                       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  HISPANIC OR LATINO                   2                40
  NOT HISPANIC OR LATINO              69               553
[1] 2 2
[1] FALSE
