[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTSARC-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/SARC-TP/11541674/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/11546379/transformed.cor.cli.txt"

nPatients in clinical file=157, in cluster file=257, common to both=156
[1]  80 156
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               124 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               124 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               124 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               124 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               144 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               144 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               146 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               146 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               137 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               137 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               139 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               139 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               117 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               117 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               25               131 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               25               131 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               56               100 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               56               100 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               46               110 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               46               110 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               125 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               125 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               126 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               30               126 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               45               111 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               45               111 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               36               120 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               36               120 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33               123 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33               123 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34               122 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34               122 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               28               128 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               28               128 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               40               116 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               40               116 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                142 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                142 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                149 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                149 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                144 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                144 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                145 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                145 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                25                131 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                25                131 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                138 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                138 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                149 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                149 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                125 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                125 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                42                114 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                42                114 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                133 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                133 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                147 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                147 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                120 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                120 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                124 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                124 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                27                129 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                27                129 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                135 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                135 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                47                109 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                47                109 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                119 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                119 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                40                116 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                40                116 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                53                103 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                53                103 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                122 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                122 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                36                120 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                36                120 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19               137 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19               137 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               134 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               134 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               134 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               134 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               49               107 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               49               107 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               116 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               116 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               33               123 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               33               123 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               125 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               125 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               24               132 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               24               132 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               32               124 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               32               124 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               142 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               142 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               21               135 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               21               135 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               118 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               118 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31               125 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31               125 
[1] "7P LOSS MUTATION ANALYSIS"
[1] 3
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               23               133 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               23               133 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               135 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               135 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34               122 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               34               122 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               129 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               27               129 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               50               106 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               50               106 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29               127 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29               127 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                73                 83 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                73                 83 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                84                 72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                84                 72 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                60                 96 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                60                 96 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                105 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                105 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                119 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                119 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                124 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                124 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                82                 74 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                82                 74 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                119 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                119 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                127 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                29                127 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                47                109 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                47                109 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                78                 78 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                78                 78 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                30                126 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                30                126 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                130 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                130 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                123 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                123 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                37                119 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                37                119 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                143 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                143 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                135 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                135 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                27                129 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                27                129 
[1] "20Q LOSS MUTATION ANALYSIS"
[1] 3
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                144 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                12                144 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                122 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                122 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                111 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                111 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59                97 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59                97 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 156 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
          NA           62         1163           NA         1116           NA 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
        1420         1802          960         1294         2271           NA 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
          NA           NA           NA           NA         1834          261 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
          NA         1809         1666           NA          702         2144 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        3289          520          610          458          540         1301 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
          NA           NA           NA         1352         1197          876 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
          NA         1952           NA          587           NA          373 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
         828          455          805         2212          763          380 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
         349         2009          713          881           63          541 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF 
         658           NA           NA         2017          716           NA 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
        1006         1085          801           NA           NA           14 
TCGA-FX-A3NJ TCGA-FX-A3NK TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
           3           NA            2          618            2            2 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
         818           NA          126           NA          729            3 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        1257          298           NA          650          272           98 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
          42          217           NA           NA          966           NA 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
        4362         3555           NA         2229           NA          688 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
         191           NA           NA         2181         1107          830 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
         356          160          118           72           15          173 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
         136          337          476            3          124         2297 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
          NA           NA           NA           NA           NA          153 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
         236           56           NA           NA           NA          553 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
         639         5324         2841         1688           NA           22 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
          NA          200          154          402           22           NA 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
          NA         2212           NA           NA           NA           NA 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        1548          525           NA          826          259          476 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
         254          268          996          749          329          376 
Variable 1:'AGE':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=49,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=101,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=16,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 156 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=54, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                0  1
  1P GAIN MUTATED   21 11
  1P GAIN WILD-TYPE 83 40
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               32               123 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               11                40 
$`1P GAIN MUTATED`
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A6YU 
        9.70        23.08        14.99        19.30        24.26        23.54 
TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       26.33         0.46        20.32        26.89         4.57         4.14 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-IF-A4AK 
       41.33         9.80        80.48         8.94        25.22        31.76 
TCGA-JV-A5VF TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A9QH TCGA-N1-A6IA TCGA-PC-A5DM 
        1.05        27.29        11.70         3.88         4.08         6.35 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XS 
        5.03        48.59         3.88         6.58         5.06        72.72 
TCGA-WK-A8XX TCGA-X6-A8C4 
       38.27         8.81 

$`1P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       59.47        54.77         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       12.49        11.47        66.05        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF 
       17.79        21.63        16.18         3.06        66.31        21.30 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3NJ TCGA-FX-A3RE 
       33.07        35.67        19.43         1.15         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EH 
        0.07         0.07        12.62        23.97         0.10        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22         1.38         7.13        37.12        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        3.91        71.70        36.39         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DK 
        5.69         4.47        11.08        15.65         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        18.08         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       46.82        18.08        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
       55.50        10.52         0.72        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
        4.80        41.49        65.46        22.62        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       18.08        27.16         8.52        15.65         8.35        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       24.62        10.82        12.36 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             0.46              0.07 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            80.48            175.04 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           13.345            18.540 
[1] "0.5 - 80.5 (13.3)"  "0.1 - 175.0 (18.5)"
[1] "hr=" "1.4"
D1V2, continuous
D1V3, binary
                   cls
clus                 0  1
  1P GAIN MUTATED   20 12
  1P GAIN WILD-TYPE 68 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED     20   12
  1P GAIN WILD-TYPE   68   56
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE              20                68
  MALE                12                56
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         3    26
  1P GAIN WILD-TYPE     5                         7    89
D1V4, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               3                 7
  WHITE                                  26                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = 1Q GAIN MUTATION ANALYSIS
D2V1, survival
                   sevent
clus2                0  1
  1Q GAIN MUTATED   24  8
  1Q GAIN WILD-TYPE 80 43
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               123 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                8                43 
$`1Q GAIN MUTATED`
TCGA-DX-A1L2 TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K 
       59.24        23.08        14.99        28.80        64.18        19.30 
TCGA-DX-A48O TCGA-DX-A6YU TCGA-DX-A8BO TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A43Z 
       27.22        23.54        26.33        20.32        26.89         4.14 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ 
        0.10        41.33         9.80        80.48         8.94        25.22 
TCGA-IF-A4AK TCGA-IW-A3M6 TCGA-K1-A42W TCGA-KF-A41W TCGA-PC-A5DN TCGA-QC-A7B5 
       31.76        22.62        27.29        11.70        38.63         5.03 
TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7WB TCGA-X6-A7WC 
       48.59         3.88        72.72        38.27        18.08        27.16 
TCGA-X6-A8C4 TCGA-X9-A971 
        8.81        12.36 

$`1Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       46.68        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       59.47        54.77         9.04        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       44.45        39.35        34.88         9.73        24.26        12.26 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       16.18         3.06        66.31        21.30        33.07        35.67 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       19.43         1.15         0.46         0.10         0.07         0.07 
TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ 
        0.07         4.57        12.62        23.97        21.37         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38         7.13        37.12        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39         5.26         3.88         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        5.69         4.47        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N 
       75.52        37.55         6.35        81.01        18.08         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        46.82        18.08        18.18        21.01       175.04 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B 
       93.40        55.50        10.52         0.72         6.58         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY 
       13.22         0.72        11.93         4.80        41.49        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       22.62        50.89        17.26         8.52        15.65         8.35 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.10              0.07 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            80.48            175.04 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            24.38             17.26 
[1] "0.1 - 80.5 (24.4)"  "0.1 - 175.0 (17.3)"
[1] "hr=" "1.5"
D2V2, continuous
D2V3, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   21 11
  1Q GAIN WILD-TYPE 67 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     21   11
  1Q GAIN WILD-TYPE   67   57
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              21                67
  MALE                11                57
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       1                         1    26
  1Q GAIN WILD-TYPE     4                         9    89
D2V4, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  26                89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = 2P GAIN MUTATION ANALYSIS
D3V1, survival
                   sevent
clus2                0  1
  2P GAIN MUTATED    6  6
  2P GAIN WILD-TYPE 98 45
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               12               143 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                6                45 
$`2P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A7EF TCGA-FX-A2QS 
       14.04         2.04        74.66        23.08        21.30         0.46 
TCGA-IW-A3M5 TCGA-KF-A41W TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-SG-A6Z7 
        5.92        11.70         0.10        37.55         5.03         3.88 

$`2P GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.24        12.85        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        12.49        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
        2.07        17.79        21.63        16.18         3.06        66.31 
TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS 
       23.54        33.07        35.67        26.33        19.43         1.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        7.13        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        13.58        73.28        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH 
        3.91        71.70        36.39        27.29         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52         6.35        38.63        81.01        18.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        7.76         1.84        46.82        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        6.58         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       72.72        41.49        38.27        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       17.26        18.08        27.16         8.52        15.65         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        32.75        24.62        10.82        12.36 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.10              0.07 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            74.66            175.04 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             8.81             19.30 
[1] "0.1 - 74.7 (8.8)"   "0.1 - 175.0 (19.3)"
[1] "hr=" "2.7"
D3V2, continuous
D3V3, binary
                   cls
clus                 0  1
  2P GAIN MUTATED    7  5
  2P GAIN WILD-TYPE 81 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      7    5
  2P GAIN WILD-TYPE   81   63
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE               7                81
  MALE                 5                63
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       1                         0     9
  2P GAIN WILD-TYPE     4                        10   106
D3V4, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                10
  WHITE                                   9               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = 2Q GAIN MUTATION ANALYSIS
D4V1, survival
                   sevent
clus2                0  1
  2Q GAIN MUTATED    7  3
  2Q GAIN WILD-TYPE 97 48
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               10               145 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                3                48 
$`2Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A6BA TCGA-DX-A7EF 
       14.04         2.04        74.66        23.08        66.05        21.30 
TCGA-DX-A8BO TCGA-KF-A41W TCGA-MO-A47R TCGA-QQ-A8VB 
       26.33        11.70         0.10       175.04 

$`2Q GAIN WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.24        12.85        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        12.49        11.47        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        66.31        23.54 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ 
       33.07        35.67        19.43         1.15         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.07        20.32         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        21.37         8.94         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH 
        3.91        71.70        36.39        27.29         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        18.18        21.01        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
        0.72         3.88         6.58         5.06        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       22.62        50.89        17.26        18.08        27.16         8.52 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       15.65         8.35         8.81        32.75        24.62        10.82 
TCGA-X9-A971 
       12.36 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.10              0.07 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           175.04            143.41 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            22.19             18.08 
[1] "0.1 - 175.0 (22.2)" "0.1 - 143.4 (18.1)"
[1] "hr=" "1.4"
D4V2, continuous
D4V3, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED    7  3
  2Q GAIN WILD-TYPE 81 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      7    3
  2Q GAIN WILD-TYPE   81   65
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE               7                81
  MALE                 3                65
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       1                         0     7
  2Q GAIN WILD-TYPE     4                        10   108
D4V4, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                10
  WHITE                                   7               108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = 3P GAIN MUTATION ANALYSIS
D5V1, survival
                   sevent
clus2                0  1
  3P GAIN MUTATED   13  6
  3P GAIN WILD-TYPE 91 45
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               19               136 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                6                45 
$`3P GAIN MUTATED`
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-DX-A8BO TCGA-HB-A2OT TCGA-IE-A3OV 
       42.77         4.54        64.18        26.33        26.89        80.48 
TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DP TCGA-QC-A7B5 
        8.94        25.22        11.70         4.47        18.08         5.03 
TCGA-QQ-A5VB TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8Y0 
       48.59         6.58         5.06         0.72        72.72        22.62 
TCGA-X6-A7WC 
       27.16 

$`3P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      108.13        17.10        20.05        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX 
       66.31        23.54        21.30        33.07        35.67        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       41.33         9.80        21.37         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       71.70        36.39        27.29         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
       75.52        37.55         6.35        38.63        81.01         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        46.82        18.08        18.18        21.01       175.04 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-UE-A6QT 
       93.40        55.50        10.52         0.72         3.88        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
       11.93         4.80        41.49        38.27        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08         8.52        15.65         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             0.72              0.07 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            80.48            175.04 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            22.62             18.13 
[1] "0.7 - 80.5 (22.6)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.1"
D5V2, continuous
D5V3, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   12  7
  3P GAIN WILD-TYPE 76 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     12    7
  3P GAIN WILD-TYPE   76   61
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              12                76
  MALE                 7                61
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       1                         2    15
  3P GAIN WILD-TYPE     4                         8   100
D5V4, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  15               100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = 3Q GAIN MUTATION ANALYSIS
D6V1, survival
                   sevent
clus2                0  1
  3Q GAIN MUTATED   12  5
  3Q GAIN WILD-TYPE 92 46
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               17               138 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                5                46 
$`3Q GAIN MUTATED`
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UF TCGA-DX-A8BO TCGA-HB-A2OT TCGA-HS-A5N8 
       42.77         4.54        64.18        26.33        26.89         0.10 
TCGA-IE-A4EI TCGA-IF-A4AJ TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VB 
        8.94        25.22        11.70        18.08         5.03        48.59 
TCGA-SG-A849 TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7WC 
        6.58         0.72        72.72        22.62        27.16 

$`3Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
      108.13        17.10        20.05        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX 
       66.31        23.54        21.30        33.07        35.67        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07         4.57         4.14        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        80.48        21.37         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       71.70        36.39        27.29         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
        7.76         1.84        46.82        18.08        18.18        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      175.04        93.40        55.50        10.52         0.72         3.88 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        5.06        13.22        11.93         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       65.46        50.89        17.26        18.08         8.52        15.65 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.35         8.81        32.75        24.62        10.82        12.36 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.10              0.07 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            72.72            175.04 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            22.62             18.13 
[1] "0.1 - 72.7 (22.6)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1"  
D6V2, continuous
D6V3, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   11  6
  3Q GAIN WILD-TYPE 77 62
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     11    6
  3Q GAIN WILD-TYPE   77   62
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              11                77
  MALE                 6                62
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       1                         1    13
  3Q GAIN WILD-TYPE     4                         9   102
D6V4, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  13               102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = 4P GAIN MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                0  1
  4P GAIN MUTATED   26 13
  4P GAIN WILD-TYPE 78 38
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               39               116 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
               13                38 
$`4P GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A48K TCGA-DX-A6BA 
       38.24        18.54        46.68        74.66        19.30        66.05 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-AATS TCGA-HB-A3YV TCGA-HS-A5N9 
        3.06        23.54        33.07         1.15         4.57        41.33 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-KF-A41W TCGA-MJ-A68H 
        7.13        25.22       143.41         6.28        11.70         4.47 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VA 
        4.08        37.55        81.01         5.03         7.76        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-AA8B 
       48.59        18.18       175.04        10.52         3.88         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C2 
       13.22         0.72        72.72        22.62        27.16        15.65 
TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
        8.81        24.62        12.36 

$`4P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        36.69        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.54         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       12.49        11.47        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO 
       21.63        16.18        66.31        21.30        35.67        26.33 
TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       19.43         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07        26.89         4.14        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        31.76        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       27.29         5.26         3.88         2.37         0.49         5.69 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
       11.08        15.65         0.10        75.52         6.35        38.63 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       18.08         1.84        46.82        21.01        93.40        55.50 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        0.72         6.58        11.93         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
       65.46        50.89        17.26        18.08         8.52         8.35 
TCGA-X6-A8C5 TCGA-X6-A8C7 
       32.75        10.82 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.72              0.07 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           175.04            116.88 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           18.180            18.755 
[1] "0.7 - 175.0 (18.2)" "0.1 - 116.9 (18.8)"
[1] "hr=" "1"  
D7V2, continuous
D7V3, binary
                   cls
clus                 0  1
  4P GAIN MUTATED   27 12
  4P GAIN WILD-TYPE 61 56
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED     27   12
  4P GAIN WILD-TYPE   61   56
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE              27                61
  MALE                12                56
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       2                         4    27
  4P GAIN WILD-TYPE     3                         6    88
D7V4, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               4                 6
  WHITE                                  27                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                0  1
  4Q GAIN MUTATED   14 11
  4Q GAIN WILD-TYPE 90 40
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               25               130 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
               11                40 
$`4Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A3LY TCGA-DX-A48K TCGA-DX-A8BL 
       38.24        18.54        46.68        17.10        19.30        33.07 
TCGA-DX-AATS TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
        1.15         4.57        41.33         3.22         7.13        25.22 
TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A7B5 
      143.41         6.28         4.47        37.55        81.01         5.03 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8Y0 
       18.08        48.59        10.52         5.06        13.22        22.62 
TCGA-X6-A8C2 
       15.65 

$`4Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        36.69        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49       108.13        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       12.49        11.47        66.05        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        66.31        23.54 
TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ 
       21.30        35.67        26.33        19.43         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z 
        0.07        20.32         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        8.94         1.38        37.12        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       71.70        36.39        27.29        11.70         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        2.37         0.49         5.69        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N 
        4.08        75.52         6.35        38.63        18.08         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
        1.84        46.82        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-UE-A6QU TCGA-WK-A8XO 
       55.50         0.72         3.88         6.58         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
        4.80        72.72        41.49        38.27        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08        27.16         8.52         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
             1.15              0.07 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           143.41            175.04 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
           18.080            18.805 
[1] "1.1 - 143.4 (18.1)" "0.1 - 175.0 (18.8)"
[1] "hr=" "1.4"
D8V2, continuous
D8V3, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED   14 11
  4Q GAIN WILD-TYPE 74 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED     14   11
  4Q GAIN WILD-TYPE   74   57
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE              14                74
  MALE                11                57
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       1                         2    18
  4Q GAIN WILD-TYPE     4                         8    97
D8V4, multiclass
                           clus
vv                          4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  18                97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                0  1
  5P GAIN MUTATED   39 17
  5P GAIN WILD-TYPE 65 34
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               56                99 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               17                34 
$`5P GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 
       38.24        46.68        31.56         6.28        17.10        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P 
        4.54        14.99        28.80        64.18        24.26        14.96 
TCGA-DX-A48R TCGA-DX-A6BG TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL 
       26.47        17.79        66.31        23.54        21.30        33.07 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 
       19.43         1.15        20.32        26.89         4.57         0.10 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A3PN 
        8.94         3.22         7.13        25.22        31.76        71.70 
TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MJ-A68H TCGA-MO-A47R 
       27.29        11.70         5.26         3.88         4.47         0.10 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
        4.08         6.35        18.08         5.03        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT 
       18.18       175.04        93.40         3.88         5.06        13.22 
TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C2 
        0.72        72.72        38.27        50.89        27.16        15.65 
TCGA-X6-A8C4 TCGA-X9-A971 
        8.81        12.36 

$`5P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04         2.04        12.85        36.69        18.54        59.24 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49       108.13        20.05        15.06        17.75 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        39.35        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       12.26        27.22        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        23.44        28.96         2.07        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
        3.06        35.67        26.33         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07         0.07         4.14        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
        9.80        80.48        21.37         1.38        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-MB-A5Y9 TCGA-MB-A5YA 
        6.28         1.05         3.91        36.39         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
        5.69        11.08        15.65        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VG 
       81.01         7.76         1.84        48.59        21.01        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
       10.52         0.72         6.58        11.93         4.80        41.49 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
       65.46        22.62        17.26        18.08         8.52         8.35 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.10              0.07 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           175.04            143.41 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            18.08             19.30 
[1] "0.1 - 175.0 (18.1)" "0.1 - 143.4 (19.3)"
[1] "hr=" "1"  
D9V2, continuous
D9V3, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   34 22
  5P GAIN WILD-TYPE 54 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     34   22
  5P GAIN WILD-TYPE   54   46
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              34                54
  MALE                22                46
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       3                         3    44
  5P GAIN WILD-TYPE     2                         7    71
D9V4, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               3                 7
  WHITE                                  44                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = 5Q GAIN MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                0  1
  5Q GAIN MUTATED   31 15
  5Q GAIN WILD-TYPE 73 36
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               46               109 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               15                36 
$`5Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3U8 TCGA-DX-A3U9 
       38.24        46.68        31.56         6.28         4.54        14.99 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6BK 
       28.80        64.18        24.26        14.96        26.47        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BX TCGA-FX-A3TO 
        3.06        66.31        23.54        33.07        19.43        20.32 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       26.89         4.57         0.10        80.48         8.94         3.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I 
       31.76       143.41        13.58        27.29        11.70         5.26 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5VA 
        4.47         0.10         4.08         6.35         5.03        18.08 
TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT 
       18.18       175.04        93.40         3.88         5.06        13.22 
TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X6-A8C4 TCGA-X9-A971 
        0.72        72.72         8.81        12.36 

$`5Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04         2.04        12.85        36.69        18.54        59.24 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       17.75        42.77        10.68        44.45        39.35        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V 
        9.73        19.30        12.26        27.22        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       12.49        11.47        66.05        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-AATS 
       17.79        21.63        21.30        35.67        26.33         1.15 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z 
        0.46         0.10         0.07         0.07         0.07         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK 
       12.62        23.97        41.33         9.80        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 
        7.13        37.12        25.22        28.21       116.88        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       36.39         3.88         2.37         0.49         5.69        11.08 
TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       15.65        75.52        37.55        38.63        81.01        18.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VG 
        7.76         1.84        46.82        48.59        21.01        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
       10.52         0.72         6.58        11.93         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        22.62        50.89        17.26        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 
       27.16         8.52        15.65         8.35        32.75        24.62 
TCGA-X6-A8C7 
       10.82 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.10              0.07 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           175.04            116.88 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           15.585            20.050 
[1] "0.1 - 175.0 (15.6)" "0.1 - 116.9 (20.1)"
[1] "hr=" "1"  
D10V2, continuous
D10V3, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED   32 14
  5Q GAIN WILD-TYPE 56 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     32   14
  5Q GAIN WILD-TYPE   56   54
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE              32                56
  MALE                14                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       3                         3    33
  5Q GAIN WILD-TYPE     2                         7    82
D10V4, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               3                 7
  WHITE                                  33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   18 13
  6P GAIN WILD-TYPE 86 38
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               31               124 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               13                38 
$`6P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U9 TCGA-DX-A6YU 
        2.04        38.24        59.24         6.28        14.99        23.54 
TCGA-DX-A7EF TCGA-DX-A8BX TCGA-DX-AATS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N8 
       21.30        19.43         1.15        26.89         4.57         0.10 
TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       41.33         3.22         7.13        37.12       143.41         5.92 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-QQ-A5VC 
        5.26         2.37         4.08         6.35        46.82        18.18 
TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X6-A8C6 
        3.88         5.06         0.72        22.62        15.65        24.62 
TCGA-X9-A971 
       12.36 

$`6P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04        12.85        36.69        18.54        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       12.49        11.47        66.05        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A8BL 
       17.79        21.63        16.18         3.06        66.31        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       35.67        26.33         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
        0.07         0.07         4.14        12.62        23.97         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         8.94         1.38        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       116.88        13.58        73.28        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W 
        1.05         3.91        71.70        36.39        27.29        11.70 
TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        3.88         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        0.10        75.52        37.55        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
        5.03         7.76         1.84        18.08        48.59        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 
      175.04        93.40        55.50        10.52         0.72         6.58 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       13.22        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       65.46        50.89        17.26        18.08        27.16         8.52 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
        8.35         8.81        32.75        10.82 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.10              0.07 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           143.41            175.04 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           12.360            20.185 
[1] "0.1 - 143.4 (12.4)" "0.1 - 175.0 (20.2)"
[1] "hr=" "2"  
D11V2, continuous
D11V3, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   20 11
  6P GAIN WILD-TYPE 68 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     20   11
  6P GAIN WILD-TYPE   68   57
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              20                68
  MALE                11                57
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       1                         2    22
  6P GAIN WILD-TYPE     4                         8    93
D11V4, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  22                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                0  1
  6Q GAIN MUTATED   18 11
  6Q GAIN WILD-TYPE 86 40
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               29               126 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               11                40 
$`6Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U9 
        2.04        38.24        18.54        23.08        17.10        14.99 
TCGA-DX-A6YU TCGA-DX-A8BX TCGA-DX-AATS TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N9 
       23.54        19.43         1.15        26.89         4.57        41.33 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-LI-A67I 
        3.22         7.13        37.12       143.41         5.92         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5VC 
        3.88         2.37         4.08        37.55         6.35        18.18 
TCGA-UE-A6QU TCGA-WK-A8XX TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X9-A971 
        0.72        38.27        15.65        24.62        12.36 

$`6Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        36.69        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL 
       21.63        16.18         3.06        66.31        21.30        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       35.67        26.33         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         0.07         4.14        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ 
        9.80        80.48        21.37         8.94         1.38        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        6.28         1.05         3.91        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       11.70         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
        0.10        75.52        38.63        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
        7.76         1.84        46.82        18.08        48.59        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      175.04        93.40        55.50        10.52         0.72         3.88 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        6.58         5.06        13.22        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       41.49        65.46        22.62        50.89        17.26        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       27.16         8.52         8.35         8.81        32.75        10.82 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.72              0.07 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           143.41            175.04 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
           15.650            20.185 
[1] "0.7 - 143.4 (15.7)" "0.1 - 175.0 (20.2)"
[1] "hr=" "1.7"
D12V2, continuous
D12V3, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   16 14
  6Q GAIN WILD-TYPE 72 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     16   14
  6Q GAIN WILD-TYPE   72   54
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              16                72
  MALE                14                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       1                         2    23
  6Q GAIN WILD-TYPE     4                         8    92
D12V4, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  23                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = 7P GAIN MUTATION ANALYSIS
D13V1, survival
                   sevent
clus2                0  1
  7P GAIN MUTATED   30 15
  7P GAIN WILD-TYPE 74 36
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               45               110 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               15                36 
$`7P GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A3LT 
       38.24        12.85        36.69        59.24        74.66        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB TCGA-DX-A6YS TCGA-DX-A6YU 
       14.99        64.18        24.26        23.44        66.31        23.54 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3RE TCGA-HB-A2OT 
       35.67        26.33        19.43         1.15         0.07        26.89 
TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK 
        4.57        41.33         8.94         3.22         7.13        31.76 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-LI-A9QH TCGA-MB-A5Y9 
      143.41        13.58         5.92         1.05         3.88         2.37 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A8VF 
        0.10        37.55        18.08         5.03        46.82        93.40 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8Y0 
       10.52         3.88         6.58         5.06         0.72        22.62 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       15.65         8.35         8.81 

$`7P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        18.54        46.68        31.56        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        59.47        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       72.72        25.08        12.49        11.47        66.05        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A7EF 
        2.07        17.79        21.63        16.18         3.06        21.30 
TCGA-DX-A8BL TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       33.07         0.46         0.10        20.32         0.07         0.07 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 
       21.37         1.38        37.12        25.22        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28        22.62         6.28         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       27.29        11.70         5.26         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
       11.08        15.65         4.08        75.52         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01         7.76         1.84        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-UE-A6QT TCGA-WK-A8XO 
       21.01       175.04        55.50         0.72        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
        4.80        72.72        41.49        38.27        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X6-A8C6 
       17.26        18.08        27.16         8.52        32.75        24.62 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.07              0.07 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           143.41            175.04 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            15.65             18.92 
[1] "0.1 - 143.4 (15.7)" "0.1 - 175.0 (18.9)"
[1] "hr=" "1.2"
D13V2, continuous
D13V3, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   28 17
  7P GAIN WILD-TYPE 60 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     28   17
  7P GAIN WILD-TYPE   60   51
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              28                60
  MALE                17                51
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       3                         2    34
  7P GAIN WILD-TYPE     2                         8    81
D13V4, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  34                81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = 7Q GAIN MUTATION ANALYSIS
D14V1, survival
                   sevent
clus2                0  1
  7Q GAIN MUTATED   24 12
  7Q GAIN WILD-TYPE 80 39
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               36               119 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               12                39 
$`7Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LT 
       38.24        12.85        36.69        59.24         6.28        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB TCGA-DX-A8BM TCGA-DX-A8BO 
       14.99        64.18        24.26        23.44        35.67        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-IE-A4EI 
       19.43         1.15         0.07        26.89         4.57         8.94 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-JV-A5VF TCGA-MB-A5Y9 
        3.22         7.13        31.76        13.58         1.05         2.37 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-SG-A849 
        0.10        37.55         5.03       175.04        93.40         6.58 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C6 
        0.72        11.93        22.62        27.16        15.65        24.62 

$`7Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        18.54        46.68        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
        8.58         9.70        59.47        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       72.72        25.08        12.49        11.47        66.05        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
        2.07        17.79        21.63        16.18         3.06        66.31 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO 
       23.54        21.30        33.07         0.46         0.10        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         0.07         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ 
       41.33         9.80        80.48        21.37         1.38        37.12 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       25.22        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62         6.28         3.91        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       11.70         5.26         3.88         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
       11.08        15.65         4.08        75.52         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        18.08         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       48.59        18.18        21.01        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        3.88         5.06        13.22         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       38.27        65.46        50.89        17.26        18.08         8.52 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
        8.35         8.81        32.75        10.82        12.36 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.07              0.07 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           175.04            143.41 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            17.54             18.18 
[1] "0.1 - 175.0 (17.5)" "0.1 - 143.4 (18.2)"
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   18 18
  7Q GAIN WILD-TYPE 70 50
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     18   18
  7Q GAIN WILD-TYPE   70   50
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              18                70
  MALE                18                50
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       2                         2    27
  7Q GAIN WILD-TYPE     3                         8    88
D14V4, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  27                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = 8P GAIN MUTATION ANALYSIS
D15V1, survival
                   sevent
clus2                0  1
  8P GAIN MUTATED   18 15
  8P GAIN WILD-TYPE 86 36
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               33               122 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               15                36 
$`8P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UF 
       14.04        12.85        74.66         4.54        14.99        64.18 
TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BX TCGA-FX-A3NJ 
       66.05         3.06        66.31        23.54        19.43         0.10 
TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3KA 
        4.57        80.48         8.94         3.22        31.76        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        5.92         1.05         3.91         4.47        11.08         0.10 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT 
        4.08        37.55         6.35         6.58         5.06        13.22 
TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-X6-A8C3 
        0.72        22.62         8.35 

$`8P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        38.24        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-AATS 
       16.18        21.30        33.07        35.67        26.33         1.15 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.46         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 
       21.37         1.38         7.13        37.12        25.22        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      143.41       116.88        73.28        22.62         6.28        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       36.39        27.29        11.70         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
        0.49         5.69        15.65        75.52        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        18.18        21.01       175.04        93.40        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       10.52         0.72         3.88        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       41.49        38.27        65.46        50.89        17.26        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       27.16         8.52        15.65         8.81        32.75        24.62 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.10              0.07 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            80.48            175.04 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            8.940            21.335 
[1] "0.1 - 80.5 (8.9)"   "0.1 - 175.0 (21.3)"
[1] "hr=" "2.4"
D15V2, continuous
D15V3, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   22 11
  8P GAIN WILD-TYPE 66 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     22   11
  8P GAIN WILD-TYPE   66   57
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              22                66
  MALE                11                57
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       4                         4    21
  8P GAIN WILD-TYPE     1                         6    94
D15V4, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               4                 6
  WHITE                                  21                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = 8Q GAIN MUTATION ANALYSIS
D16V1, survival
                   sevent
clus2                0  1
  8Q GAIN MUTATED   18 16
  8Q GAIN WILD-TYPE 86 35
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               34               121 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               16                35 
$`8Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       14.04        12.85        74.66         4.54        14.99        10.68 
TCGA-DX-A3UF TCGA-DX-A6BA TCGA-DX-A6YU TCGA-DX-A8BO TCGA-DX-A8BX TCGA-FX-A2QS 
       64.18        66.05        23.54        26.33        19.43         0.46 
TCGA-FX-A3NJ TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IF-A4AJ 
        0.10         4.57        41.33        80.48         8.94        25.22 
TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-MJ-A68H TCGA-MJ-A68J 
       31.76         5.92         1.05         3.91         4.47        11.08 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-SG-A849 
        0.10         4.08        37.55        48.59         3.88         6.58 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8Y0 TCGA-X6-A8C3 
       13.22         0.72        22.62         8.35 

$`8Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        38.24        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       15.06        17.75        42.77        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-AATS 
        3.06        66.31        21.30        33.07        35.67         1.15 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z 
        0.07        20.32         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ 
       12.62        23.97         0.10         9.80        21.37         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38         7.13        37.12        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        22.62         6.28        71.70        36.39 
TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA 
       27.29        11.70         5.26         3.88         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        5.69        15.65        75.52         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.18        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        0.72         5.06        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.52        15.65         8.81        32.75        24.62        10.82 
TCGA-X9-A971 
       12.36 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.10              0.07 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            80.48            175.04 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           11.965            20.320 
[1] "0.1 - 80.5 (12.0)"  "0.1 - 175.0 (20.3)"
[1] "hr=" "2.3"
D16V2, continuous
D16V3, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   24 10
  8Q GAIN WILD-TYPE 64 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     24   10
  8Q GAIN WILD-TYPE   64   58
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              24                64
  MALE                10                58
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       4                         4    22
  8Q GAIN WILD-TYPE     1                         6    93
D16V4, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   4                 1
  BLACK OR AFRICAN AMERICAN               4                 6
  WHITE                                  22                93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = 9P GAIN MUTATION ANALYSIS
D17V1, survival
                   sevent
clus2                0  1
  9P GAIN MUTATED   16 12
  9P GAIN WILD-TYPE 88 39
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               28               127 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               12                39 
$`9P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A3LU TCGA-DX-A3U9 
        2.04        38.24        36.69        59.24        70.49        14.99 
TCGA-DX-A3UA TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6BB TCGA-DX-A6YU TCGA-DX-A8BL 
       10.68        24.26        12.26        23.44        23.54        33.07 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3TO TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3KA 
       19.43         1.15        20.32         7.13        31.76        13.58 
TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-SG-A6Z7 
        1.05        11.70         5.26        18.08        46.82         3.88 
TCGA-SG-A849 TCGA-WK-A8XO TCGA-WK-A8XS TCGA-X6-A8C6 
        6.58        11.93        72.72        24.62 

$`9P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        18.54        46.68        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       42.77         4.54        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       64.18         9.73        19.30        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       72.72        25.08        12.49        11.47        66.05        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
        2.07        17.79        21.63        16.18         3.06        66.31 
TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       21.30        35.67        26.33         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 
        8.94         3.22         1.38        37.12        25.22        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        73.28         5.92        22.62         6.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A9QH TCGA-MB-A5Y9 
        3.91        71.70        36.39        27.29         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         7.76         1.84        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        5.06        13.22         0.72         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46        22.62        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
        8.52        15.65         8.35         8.81        32.75        10.82 
TCGA-X9-A971 
       12.36 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             1.05              0.07 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            72.72            175.04 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           18.755            18.180 
[1] "1.1 - 72.7 (18.8)"  "0.1 - 175.0 (18.2)"
[1] "hr=" "1.7"
D17V2, continuous
D17V3, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   15 13
  9P GAIN WILD-TYPE 73 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     15   13
  9P GAIN WILD-TYPE   73   55
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              15                73
  MALE                13                55
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         1    23
  9P GAIN WILD-TYPE     5                         9    92
D17V4, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  23                92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                0  1
  9Q GAIN MUTATED   29 11
  9Q GAIN WILD-TYPE 75 40
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               40               115 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               11                40 
$`9Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R 
        2.04        38.24        36.69        46.68        59.24        74.66 
TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48N 
       70.49        20.05        42.77        14.99        10.68        12.26 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BO 
       66.05        23.44         3.06        23.54        33.07        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3TO TCGA-IE-A4EI TCGA-IE-A4EJ 
       19.43         1.15         0.46        20.32         8.94         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        7.13        31.76         1.05        11.70         5.26         3.88 
TCGA-MB-A5Y9 TCGA-PC-A5DP TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-SG-A849 TCGA-WK-A8XO 
        2.37        18.08        46.82        18.18         6.58        11.93 
TCGA-WK-A8XS TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
       72.72        15.65         8.35        12.36 

$`9Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        18.54        31.56        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        23.08       108.13 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.10        15.06        17.75         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BM TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       66.31        21.30        35.67         0.10         0.07         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
        0.10        41.33         9.80        80.48        21.37         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        25.22        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92        22.62         6.28         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       36.39        27.29         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       38.63        81.01         5.03         7.76         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ 
        0.72         3.88         5.06        13.22         0.72         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46        22.62        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08        27.16         8.52         8.81        32.75        24.62 
TCGA-X6-A8C7 
       10.82 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.46              0.07 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            74.66            175.04 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           16.865            19.300 
[1] "0.5 - 74.7 (16.9)"  "0.1 - 175.0 (19.3)"
[1] "hr=" "1"  
D18V2, continuous
D18V3, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   23 17
  9Q GAIN WILD-TYPE 65 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     23   17
  9Q GAIN WILD-TYPE   65   51
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              23                65
  MALE                17                51
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       1                         1    31
  9Q GAIN WILD-TYPE     4                         9    84
D18V4, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  31                84
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = 10P GAIN MUTATION ANALYSIS
D19V1, survival
                    sevent
clus2                 0  1
  10P GAIN MUTATED    7  7
  10P GAIN WILD-TYPE 97 44
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                14                141 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 7                 44 
$`10P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A8BL TCGA-HS-A5N9 TCGA-IE-A6BZ 
       14.04        42.77         4.54        33.07        41.33         7.13 
TCGA-IS-A3KA TCGA-JV-A5VF TCGA-LI-A67I TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-WK-A8Y0 
       13.58         1.05         5.26        18.08        18.08        22.62 
TCGA-X6-A8C2 TCGA-X6-A8C6 
       15.65        24.62 

$`10P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UA 
       17.10        20.05        15.06        17.75        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX 
       66.31        23.54        21.30        35.67        26.33        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        73.28         5.92        22.62         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 
       71.70        36.39        27.29        11.70         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         7.76         1.84        46.82        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
        4.80        72.72        41.49        38.27        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08        27.16         8.52         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        10.82        12.36 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              1.05               0.07 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             42.77             175.04 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
            16.865             19.300 
[1] "1.1 - 42.8 (16.9)"  "0.1 - 175.0 (19.3)"
[1] "hr=" "2.2"
D19V2, continuous
D19V3, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    8  6
  10P GAIN WILD-TYPE 80 62
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      8    6
  10P GAIN WILD-TYPE   80   62
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                8                 80
  MALE                  6                 62
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         1    11
  10P GAIN WILD-TYPE     5                         9   104
D19V4, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = 10Q GAIN MUTATION ANALYSIS
D20V1, survival
                    sevent
clus2                  0   1
  10Q GAIN MUTATED     4   3
  10Q GAIN WILD-TYPE 100  48
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 7                148 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 3                 48 
$`10Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A3U8 TCGA-DX-A8BL TCGA-DX-A8BM TCGA-HS-A5N9 TCGA-SG-A6Z7 
       14.04         4.54        33.07        35.67        41.33         3.88 
TCGA-X6-A8C6 
       24.62 

$`10Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75        42.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BO TCGA-DX-A8BX 
        3.06        66.31        23.54        21.30        26.33        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        6.28         1.05         3.91        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       11.70         5.26         3.88         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        4.47        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
       37.55         6.35        38.63        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        7.76         1.84        46.82        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        6.58         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       72.72        41.49        38.27        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       17.26        18.08        27.16         8.52        15.65         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        32.75        10.82        12.36 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
              3.88               0.07 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             41.33             175.04 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             24.62              18.13 
[1] "3.9 - 41.3 (24.6)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.6"
D20V2, continuous
D20V3, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    2  5
  10Q GAIN WILD-TYPE 86 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      2    5
  10Q GAIN WILD-TYPE   86   63
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                2                 86
  MALE                  5                 63
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     5
  10Q GAIN WILD-TYPE     5                        10   110
D20V4, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                    5                110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = 11P GAIN MUTATION ANALYSIS
D21V1, survival
                    sevent
clus2                  0   1
  11P GAIN MUTATED     4   8
  11P GAIN WILD-TYPE 100  43
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                12                143 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 8                 43 
$`11P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A6BK TCGA-DX-A7EF TCGA-DX-AATS TCGA-IE-A4EJ TCGA-IS-A3KA 
       14.04        16.18        21.30         1.15         3.22        13.58 
TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A8VH TCGA-X6-A8C3 
       11.70        18.08         5.03        18.08        10.52         8.35 

$`11P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
        3.06        66.31        23.54        33.07        35.67        26.33 
TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       19.43         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37         8.94 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        27.29         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        3.88         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       38.63        81.01         7.76         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       18.18        21.01       175.04        93.40        55.50         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       50.89        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        32.75        24.62        10.82        12.36 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              1.15               0.07 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             21.30             175.04 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             12.64              20.32 
[1] "1.1 - 21.3 (12.6)"  "0.1 - 175.0 (20.3)"
[1] "hr=" "5.5"
D21V2, continuous
D21V3, binary
                    cls
clus                  0  1
  11P GAIN MUTATED    9  3
  11P GAIN WILD-TYPE 79 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      9    3
  11P GAIN WILD-TYPE   79   65
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE                9                 79
  MALE                  3                 65
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       1                         0    11
  11P GAIN WILD-TYPE     4                        10   104
D21V4, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = 11Q GAIN MUTATION ANALYSIS
D22V1, survival
                    sevent
clus2                  0   1
  11Q GAIN MUTATED     4   7
  11Q GAIN WILD-TYPE 100  44
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                11                144 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 7                 44 
$`11Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A48L TCGA-DX-A7EF TCGA-DX-AATS TCGA-HB-A43Z TCGA-IE-A4EH 
       14.04        24.26        21.30         1.15         4.14        21.37 
TCGA-KF-A41W TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A8VH 
       11.70        18.08         5.03        18.08        10.52 

$`11Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        2.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
        3.06        66.31        23.54        33.07        35.67        26.33 
TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       19.43         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07        26.89         4.57        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33         9.80        80.48         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        7.13        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        27.29         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        3.88         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       38.63        81.01         7.76         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       18.18        21.01       175.04        93.40        55.50         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       50.89        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.35         8.81        32.75        24.62        10.82        12.36 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              1.15               0.07 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
             24.26             175.04 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            14.040             19.365 
[1] "1.1 - 24.3 (14.0)"  "0.1 - 175.0 (19.4)"
[1] "hr=" "4.2"
D22V2, continuous
D22V3, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED    8  3
  11Q GAIN WILD-TYPE 80 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      8    3
  11Q GAIN WILD-TYPE   80   65
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE                8                 80
  MALE                  3                 65
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         0    11
  11Q GAIN WILD-TYPE     5                        10   104
D22V4, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = 12P GAIN MUTATION ANALYSIS
D23V1, survival
                    sevent
clus2                 0  1
  12P GAIN MUTATED   14 11
  12P GAIN WILD-TYPE 90 40
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                25                130 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                11                 40 
$`12P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3LS TCGA-DX-A6YS TCGA-DX-A8BX 
       14.04        38.24        12.85         9.04        66.31        19.43 
TCGA-DX-AATS TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-K1-A42W 
        1.15         4.57         0.10        25.22         5.92        27.29 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VH 
        2.37         0.10        37.55        18.08        93.40        10.52 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 
        6.58         5.06         0.72        15.65         8.81        24.62 
TCGA-X9-A971 
       12.36 

$`12P GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        36.69        18.54        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        12.49        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU 
        2.07        17.79        21.63        16.18         3.06        23.54 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3NJ 
       21.30        33.07        35.67        26.33         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z 
        0.07        20.32         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        8.94         3.22         1.38         7.13        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 
       28.21       143.41       116.88        13.58        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
        6.28         1.05         3.91        71.70        36.39        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         3.88         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
       15.65         4.08        75.52         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       18.08         5.03         7.76         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 
       18.18        21.01       175.04        55.50         0.72         3.88 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       13.22        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46        22.62        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
        8.52         8.35        32.75        10.82 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              0.10               0.07 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
             93.40             175.04 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            12.360             20.665 
[1] "0.1 - 93.4 (12.4)"  "0.1 - 175.0 (20.7)"
[1] "hr=" "2.1"
D23V2, continuous
D23V3, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   13 12
  12P GAIN WILD-TYPE 75 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     13   12
  12P GAIN WILD-TYPE   75   56
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               13                 75
  MALE                 12                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       2                         0    20
  12P GAIN WILD-TYPE     3                        10    95
D23V4, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   20                 95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = 12Q GAIN MUTATION ANALYSIS
D24V1, survival
                    sevent
clus2                 0  1
  12Q GAIN MUTATED   12  6
  12Q GAIN WILD-TYPE 92 45
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                18                137 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 45 
$`12Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A6YS TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS 
       38.24        66.31        33.07        26.33        19.43         1.15 
TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IF-A4AJ TCGA-MO-A47R TCGA-PC-A5DL 
        4.57         0.10        41.33        25.22         0.10        37.55 
TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A849 TCGA-UE-A6QU TCGA-X6-A8C3 TCGA-X6-A8C6 
       93.40        10.52         6.58         0.72         8.35        24.62 

$`12Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BM TCGA-FX-A2QS 
       16.18         3.06        23.54        21.30        35.67         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        4.14        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        8.94         3.22         1.38         7.13        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62         6.28         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA 
       27.29        11.70         5.26         3.88         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08        15.65         4.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N 
        6.35        38.63        81.01        18.08         5.03         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT 
      175.04        55.50         0.72         3.88         5.06        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       22.62        50.89        17.26        18.08        27.16         8.52 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       15.65         8.81        32.75        10.82        12.36 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              0.10               0.07 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
             93.40             175.04 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            22.025             18.080 
[1] "0.1 - 93.4 (22.0)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED    9  9
  12Q GAIN WILD-TYPE 79 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      9    9
  12Q GAIN WILD-TYPE   79   59
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE                9                 79
  MALE                  9                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       3                         0    12
  12Q GAIN WILD-TYPE     2                        10   103
D24V4, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   12                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = 13Q GAIN MUTATION ANALYSIS
D25V1, survival
                    sevent
clus2                 0  1
  13Q GAIN MUTATED    6  1
  13Q GAIN WILD-TYPE 98 50
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 7                148 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                 1                 50 
$`13Q GAIN MUTATED`
TCGA-HS-A5N9 TCGA-IF-A4AK TCGA-JV-A5VE TCGA-LI-A9QH TCGA-MJ-A68H TCGA-PC-A5DP 
       41.33        31.76         6.28         3.88         4.47        18.08 
TCGA-X9-A971 
       12.36 

$`13Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF 
       21.63        16.18         3.06        66.31        23.54        21.30 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
       33.07        35.67        26.33        19.43         1.15         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        21.37         8.94         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        25.22        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92        22.62         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       36.39        27.29        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55         6.35        38.63        81.01         5.03         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      175.04        93.40        55.50        10.52         0.72         3.88 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        6.58         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       72.72        41.49        38.27        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       17.26        18.08        27.16         8.52        15.65         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.81        32.75        24.62        10.82 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              3.88               0.07 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             41.33             175.04 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             12.36              18.92 
[1] "3.9 - 41.3 (12.4)"  "0.1 - 175.0 (18.9)"
[1] "hr=" "1.5"
D25V2, continuous
D25V3, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED    7  0
  13Q GAIN WILD-TYPE 81 68
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      7    0
  13Q GAIN WILD-TYPE   81   68
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE                7                 81
  MALE                  0                 68
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         2     4
  13Q GAIN WILD-TYPE     5                         8   111
D25V4, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                    4                111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = 14Q GAIN MUTATION ANALYSIS
D26V1, survival
                    sevent
clus2                 0  1
  14Q GAIN MUTATED   15 16
  14Q GAIN WILD-TYPE 89 35
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                31                124 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                16                 35 
$`14Q GAIN MUTATED`
TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A3LW TCGA-DX-A3U9 TCGA-DX-A3UF 
       46.68         6.28        60.30       108.13        14.99        64.18 
TCGA-DX-A48L TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IF-A4AJ 
       24.26         3.06        21.30         4.57        12.62        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A8JL 
       31.76        13.58         5.92        11.70         2.37         5.69 
TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        4.47         6.35        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A8C3 
       93.40         3.88         6.58        72.72        22.62         8.35 
TCGA-X9-A971 
       12.36 

$`14Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08        70.49        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       16.18        66.31        23.54        33.07        35.67        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       19.43         1.15         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         0.07        26.89         4.14        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38         7.13        37.12        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MJ-A68J 
       36.39        27.29         5.26         3.88         0.49        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
       15.65         0.10         4.08        75.52        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-AA8B TCGA-UE-A6QT 
      175.04        55.50        10.52         0.72         5.06        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
        0.72        11.93         4.80        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       50.89        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.81        32.75        24.62        10.82 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
              2.37               0.07 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            108.13             175.04 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
            14.990             19.365 
[1] "2.4 - 108.1 (15.0)" "0.1 - 175.0 (19.4)"
[1] "hr=" "1.9"
D26V2, continuous
D26V3, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED   19 12
  14Q GAIN WILD-TYPE 69 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED     19   12
  14Q GAIN WILD-TYPE   69   56
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE               19                 69
  MALE                 12                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       1                         1    25
  14Q GAIN WILD-TYPE     4                         9    90
D26V4, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = 15Q GAIN MUTATION ANALYSIS
D27V1, survival
                    sevent
clus2                 0  1
  15Q GAIN MUTATED   28 14
  15Q GAIN WILD-TYPE 76 37
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                42                113 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                14                 37 
$`15Q GAIN MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L4 TCGA-DX-A23U TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3U7 
       38.24        42.54        76.41         6.28         8.58        42.77 
TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6YS 
       14.99        39.35        64.18        24.26        66.05        66.31 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EI 
       26.33        19.43         4.14        12.62        41.33         8.94 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-JV-A75J 
        3.22         7.13        25.22        31.76        13.58         3.91 
TCGA-K1-A42W TCGA-LI-A67I TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QQ-A5V9 
       27.29         5.26         4.47        37.55        18.08        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SG-A849 
       18.08        18.18        21.01        93.40         3.88         6.58 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 
        5.06         0.72        72.72         8.35         8.81        12.36 

$`15Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Z 
       59.24        31.56        74.66         5.26        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        44.45        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        12.49        11.47        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A7EF 
       17.79        21.63        16.18         3.06        23.54        21.30 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       33.07        35.67         1.15         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 
       20.32         0.07         0.07        26.89         4.57        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ 
        0.10         9.80        80.48        21.37         1.38        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A9QH 
        6.28         1.05        71.70        36.39        11.70         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        2.37         0.49         5.69        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        4.08        75.52         6.35        38.63        81.01         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH 
        7.76         1.84        48.59       175.04        55.50        10.52 
TCGA-RN-A68Q TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        0.72        13.22        11.93         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46        22.62        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.52        15.65        32.75        24.62        10.82 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              0.72               0.07 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             93.40             175.04 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             18.13              18.54 
[1] "0.7 - 93.4 (18.1)"  "0.1 - 175.0 (18.5)"
[1] "hr=" "1"  
D27V2, continuous
D27V3, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED   29 13
  15Q GAIN WILD-TYPE 59 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED     29   13
  15Q GAIN WILD-TYPE   59   55
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE               29                 59
  MALE                 13                 55
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       2                         1    33
  15Q GAIN WILD-TYPE     3                         9    82
D27V4, multiclass
                           clus
vv                          15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   33                 82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   12 11
  16P GAIN WILD-TYPE 92 40
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                23                132 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                11                 40 
$`16P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A2J0 TCGA-DX-A3U5 TCGA-DX-A3U9 
       14.04         2.04        38.24         9.70        15.06        14.99 
TCGA-DX-A48L TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       24.26        66.31        23.54        21.30        33.07        35.67 
TCGA-FX-A2QS TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA 
        0.46        80.48        21.37        25.22        31.76        13.58 
TCGA-IW-A3M5 TCGA-LI-A67I TCGA-MO-A47R TCGA-SG-A6Z7 TCGA-X2-A95T 
        5.92         5.26         0.10         3.88        50.89 

$`16P GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        36.69        18.54        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 
       23.08        70.49       108.13        17.10        20.05        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3NJ 
       16.18         3.06        26.33        19.43         1.15         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.07        20.32         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 
        8.94         3.22         1.38         7.13        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      143.41       116.88        73.28        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A9QH 
        3.91        71.70        36.39        27.29        11.70         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        18.18        21.01       175.04        93.40        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
       10.52         0.72         6.58         5.06        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.35         8.81        32.75        24.62        10.82        12.36 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.10               0.07 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             80.48             175.04 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             21.30              18.13 
[1] "0.1 - 80.5 (21.3)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.8"
D28V2, continuous
D28V3, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   13 10
  16P GAIN WILD-TYPE 75 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     13   10
  16P GAIN WILD-TYPE   75   58
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               13                 75
  MALE                 10                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       1                         0    19
  16P GAIN WILD-TYPE     4                        10    96
D28V4, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                  0   1
  16Q GAIN MUTATED     3   6
  16Q GAIN WILD-TYPE 101  45
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 9                146 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 45 
$`16Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A3U5 TCGA-DX-A6YU TCGA-DX-A7EF TCGA-IE-A3OV TCGA-IS-A3K7 
        2.04        15.06        23.54        21.30        80.48       143.41 
TCGA-IW-A3M5 TCGA-SG-A6Z7 TCGA-WK-A8Y0 
        5.92         3.88        22.62 

$`16Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX 
        3.06        66.31        33.07        35.67        26.33        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33         9.80        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        13.58        73.28        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I 
        3.91        71.70        36.39        27.29        11.70         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        3.88         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        81.01        18.08         5.03         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        18.18        21.01       175.04 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B 
       93.40        55.50        10.52         0.72         6.58         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       13.22         0.72        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
        8.52        15.65         8.35         8.81        32.75        24.62 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              2.04               0.07 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
            143.41             175.04 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             21.30              18.13 
[1] "2.0 - 143.4 (21.3)" "0.1 - 175.0 (18.1)"
[1] "hr=" "1.8"
D29V2, continuous
D29V3, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED    6  3
  16Q GAIN WILD-TYPE 82 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      6    3
  16Q GAIN WILD-TYPE   82   65
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE                6                 82
  MALE                  3                 65
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         0     8
  16Q GAIN WILD-TYPE     5                        10   107
D29V4, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                    8                107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = 17P GAIN MUTATION ANALYSIS
D30V1, survival
                    sevent
clus2                 0  1
  17P GAIN MUTATED   24 12
  17P GAIN WILD-TYPE 80 39
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                36                119 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                12                 39 
$`17P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3UF 
        2.04        12.85        46.68        59.24         6.28        64.18 
TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A8BL TCGA-DX-A8BM 
       19.30        26.47         2.07        16.18        33.07        35.67 
TCGA-DX-A8BO TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 
       26.33         0.07        20.32         0.07         4.57        12.62 
TCGA-JV-A75J TCGA-LI-A67I TCGA-LI-A9QH TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DP 
        3.91         5.26         3.88         0.10         4.08        18.08 
TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-SG-A849 TCGA-UE-A6QU TCGA-WK-A8XS 
        5.03        46.82        18.08         6.58         0.72        72.72 
TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X9-A971 
       22.62        27.16        15.65         8.35        24.62        12.36 

$`17P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        38.24        36.69        18.54        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       28.80        34.88         9.73        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS 
       23.44        28.96        17.79        21.63         3.06        66.31 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ 
       23.54        21.30        19.43         1.15         0.46         0.10 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.07        26.89         4.14        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        7.13        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-MB-A5Y9 
        1.05        71.70        36.39        27.29        11.70         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-PC-A5DK 
        0.49         5.69         4.47        11.08        15.65        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55         6.35        38.63        81.01         7.76         1.84 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        18.18        21.01       175.04        93.40        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO 
       10.52         0.72         3.88         5.06        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
        4.80        41.49        38.27        65.46        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.08         8.52         8.81        32.75        10.82 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              0.07               0.07 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             72.72             175.04 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             14.25              21.01 
[1] "0.1 - 72.7 (14.2)"  "0.1 - 175.0 (21.0)"
[1] "hr=" "1.6"
D30V2, continuous
D30V3, binary
                    cls
clus                  0  1
  17P GAIN MUTATED   19 17
  17P GAIN WILD-TYPE 69 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED     19   17
  17P GAIN WILD-TYPE   69   51
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE               19                 69
  MALE                 17                 51
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       3                         1    27
  17P GAIN WILD-TYPE     2                         9    88
D30V4, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   27                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                 0  1
  17Q GAIN MUTATED   24  8
  17Q GAIN WILD-TYPE 80 43
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                32                123 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 8                 43 
$`17Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A6BF TCGA-DX-A6BK 
        2.04        59.24        10.68        19.30         2.07        16.18 
TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A3RE TCGA-FX-A3TO 
       23.54        33.07        35.67        26.33         0.07        20.32 
TCGA-FX-A48G TCGA-HB-A5W3 TCGA-IE-A6BZ TCGA-IW-A3M4 TCGA-JV-A75J TCGA-LI-A67I 
        0.07        12.62         7.13        73.28         3.91         5.26 
TCGA-LI-A9QH TCGA-MO-A47R TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VC 
        3.88         0.10        18.08         5.03        18.08        18.18 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A8C2 
        6.58         5.06         0.72        72.72        22.62        15.65 
TCGA-X6-A8C3 TCGA-X9-A971 
        8.35        12.36 

$`17Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       20.05        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        12.49        11.47        66.05        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BX 
       17.79        21.63         3.06        66.31        21.30        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        1.15         0.46         0.10         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.14        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37         8.94         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 
       31.76        28.21       143.41       116.88        13.58         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62         6.28         1.05        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       11.70         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       15.65         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD 
       81.01         7.76         1.84        46.82        48.59        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      175.04        93.40        55.50        10.52         0.72         3.88 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       13.22        11.93         4.80        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C4 
       50.89        17.26        18.08        27.16         8.52         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.07               0.07 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             73.28             175.04 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             12.49              21.37 
[1] "0.1 - 73.3 (12.5)"  "0.1 - 175.0 (21.4)"
[1] "hr=" "1.2"
D31V2, continuous
D31V3, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   23  9
  17Q GAIN WILD-TYPE 65 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     23    9
  17Q GAIN WILD-TYPE   65   59
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               23                 65
  MALE                  9                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       3                         0    27
  17Q GAIN WILD-TYPE     2                        10    88
D31V4, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   27                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = 18P GAIN MUTATION ANALYSIS
D32V1, survival
                    sevent
clus2                 0  1
  18P GAIN MUTATED   18  9
  18P GAIN WILD-TYPE 86 42
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                27                128 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 9                 42 
$`18P GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3UE TCGA-DX-A6BA 
        2.04        31.56         6.28        42.77        34.88        66.05 
TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-AATS TCGA-FX-A3TO TCGA-HB-A43Z 
       23.54        35.67        26.33         1.15        20.32         4.14 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
        0.10         8.94         7.13        13.58         5.92         6.28 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5V9 
        3.88         2.37         0.10         6.35         7.76        46.82 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A971 
       27.16         8.35        12.36 

$`18P GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        38.24        12.85        36.69        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        28.80        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       12.49        11.47        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL 
       21.63        16.18         3.06        66.31        21.30        33.07 
TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       19.43         0.46         0.10         0.07         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       26.89         4.57        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         3.22         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       143.41       116.88        73.28        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W 
        1.05         3.91        71.70        36.39        27.29        11.70 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        5.26         0.49         5.69         4.47        11.08        15.65 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52        37.55        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.03         1.84        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      175.04        93.40        55.50        10.52         0.72         3.88 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        6.58         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       72.72        41.49        38.27        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       17.26        18.08         8.52        15.65         8.81        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 
       24.62        10.82 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              0.10               0.07 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             66.05             175.04 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              8.35              19.74 
[1] "0.1 - 66.0 (8.3)"   "0.1 - 175.0 (19.7)"
[1] "hr=" "1.7"
D32V2, continuous
D32V3, binary
                    cls
clus                  0  1
  18P GAIN MUTATED   17 10
  18P GAIN WILD-TYPE 71 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED     17   10
  18P GAIN WILD-TYPE   71   58
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE               17                 71
  MALE                 10                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       2                         2    19
  18P GAIN WILD-TYPE     3                         8    96
D32V4, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   19                 96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = 18Q GAIN MUTATION ANALYSIS
D33V1, survival
                    sevent
clus2                 0  1
  18Q GAIN MUTATED   14  7
  18Q GAIN WILD-TYPE 90 44
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                21                134 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 7                 44 
$`18Q GAIN MUTATED`
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A3U7 TCGA-DX-A3UE TCGA-DX-A6YU TCGA-DX-AATS 
       59.24        31.56        42.77        34.88        23.54         1.15 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A6BZ 
        0.46        20.32         4.14         0.10         8.94         7.13 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL 
       13.58         5.92         6.28         2.37         0.10        37.55 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-X9-A971 
        7.76        46.82        12.36 

$`18Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       46.68        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        12.49        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
        2.07        17.79        21.63        16.18         3.06        66.31 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-FX-A3NJ 
       21.30        33.07        35.67        26.33        19.43         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 
        0.07         0.07         0.07        26.89         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ 
       23.97        41.33         9.80        80.48        21.37         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
      116.88        73.28        22.62         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA 
       36.39        27.29        11.70         5.26         3.88         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08        15.65         4.08        75.52 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 
        6.35        38.63        81.01        18.08         5.03         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       18.08        48.59        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B 
       55.50        10.52         0.72         3.88         6.58         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       13.22         0.72        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        22.62        50.89        17.26        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       27.16         8.52        15.65         8.35         8.81        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 
       24.62        10.82 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              0.10               0.07 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             59.24             175.04 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             8.940             19.365 
[1] "0.1 - 59.2 (8.9)"   "0.1 - 175.0 (19.4)"
[1] "hr=" "1.6"
D33V2, continuous
D33V3, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED   14  7
  18Q GAIN WILD-TYPE 74 61
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED     14    7
  18Q GAIN WILD-TYPE   74   61
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE               14                 74
  MALE                  7                 61
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         2    15
  18Q GAIN WILD-TYPE     4                         8   100
D33V4, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   15                100
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = 19P GAIN MUTATION ANALYSIS
D34V1, survival
                    sevent
clus2                 0  1
  19P GAIN MUTATED   27 20
  19P GAIN WILD-TYPE 77 31
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                47                108 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                20                 31 
$`19P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3U7 TCGA-DX-A3U9 
       59.24        74.66         6.28         9.70        42.77        14.99 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       64.18        12.26        66.31        21.30        33.07        35.67 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       26.33        19.43         1.15         0.07        20.32         0.07 
TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
        4.57         9.80        80.48         8.94         3.22         7.13 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A42W TCGA-LI-A9QH TCGA-QQ-A5V9 
        5.92         1.05         3.91        27.29         3.88        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-SG-A849 TCGA-UE-A6QT 
       18.08        18.18       175.04        93.40         6.58        13.22 
TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7WB TCGA-X6-A7WC 
        0.72        72.72        38.27        18.08        27.16 

$`19P GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       36.69        31.56        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A2OT 
        3.06        23.54         0.46         0.10         0.07        26.89 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EH 
        4.14        12.62        23.97         0.10        41.33        21.37 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      116.88        13.58        73.28        22.62         6.28        71.70 
TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        11.70         5.26         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        4.47        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
       37.55         6.35        38.63        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
        7.76         1.84        48.59        21.01        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        0.72         3.88         5.06        11.93         4.80        41.49 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 
       65.46        22.62        50.89        17.26         8.52        15.65 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.35         8.81        32.75        24.62        10.82        12.36 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.07               0.07 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            175.04             143.41 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            18.080             19.675 
[1] "0.1 - 175.0 (18.1)" "0.1 - 143.4 (19.7)"
[1] "hr=" "1.5"
D34V2, continuous
D34V3, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   24 23
  19P GAIN WILD-TYPE 64 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     24   23
  19P GAIN WILD-TYPE   64   45
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               24                 64
  MALE                 23                 45
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       2                         1    34
  19P GAIN WILD-TYPE     3                         9    81
D34V4, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   34                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = 19Q GAIN MUTATION ANALYSIS
D35V1, survival
                    sevent
clus2                 0  1
  19Q GAIN MUTATED   24 13
  19Q GAIN WILD-TYPE 80 38
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                37                118 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                13                 38 
$`19Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        38.24        12.85        46.68        59.24 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6YS 
       74.66         6.28        14.99        64.18        12.26        66.31 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-AATS 
       23.54        21.30        33.07        35.67        19.43         1.15 
TCGA-FX-A3TO TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       20.32         4.57         9.80         8.94         3.22         7.13 
TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A9QH TCGA-MJ-A68H TCGA-QQ-A5VA TCGA-QQ-A5VB 
        1.05        11.70         3.88         4.47        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A849 TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X6-A7WC 
       18.18        93.40         6.58         0.72        72.72        27.16 
TCGA-X6-A8C3 
        8.35 

$`19Q GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       36.69        18.54        31.56        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       12.49        11.47        66.05        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A8BO TCGA-FX-A2QS 
       17.79        21.63        16.18         3.06        26.33         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z 
        0.10         0.07         0.07         0.07        26.89         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10        41.33        80.48        21.37 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-MB-A5Y9 
        3.91        71.70        36.39        27.29         5.26         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       75.52        37.55         6.35        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VB 
        5.03         7.76         1.84        46.82        21.01       175.04 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-UE-A6QT 
       55.50        10.52         0.72         3.88         5.06        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        41.49        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 
       50.89        17.26        18.08         8.52        15.65         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.72               0.07 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             93.40             175.04 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            14.990             19.675 
[1] "0.7 - 93.4 (15.0)"  "0.1 - 175.0 (19.7)"
[1] "hr=" "1.2"
D35V2, continuous
D35V3, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   20 17
  19Q GAIN WILD-TYPE 68 51
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     20   17
  19Q GAIN WILD-TYPE   68   51
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               20                 68
  MALE                 17                 51
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       2                         2    25
  19Q GAIN WILD-TYPE     3                         8    90
D35V4, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = 20P GAIN MUTATION ANALYSIS
D36V1, survival
                    sevent
clus2                 0  1
  20P GAIN MUTATED   23 17
  20P GAIN WILD-TYPE 81 34
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                40                115 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                17                 34 
$`20P GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
       14.04         2.04        38.24        18.54        46.68        74.66 
TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A48P TCGA-DX-A6BB TCGA-DX-A6YQ 
        6.28        42.77        10.68        14.96        23.44         3.06 
TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3NJ TCGA-FX-A3TO 
       23.54        33.07        19.43         1.15         0.10        20.32 
TCGA-FX-A48G TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ 
        0.07        12.62        41.33        80.48         3.22        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A9QH 
       31.76        13.58         5.92        27.29        11.70         3.88 
TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-SG-A6Z7 TCGA-UE-A6QU 
        2.37         4.08        37.55         5.03         3.88         0.72 
TCGA-WK-A8XX TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 
       38.27        27.16         8.35        24.62 

$`20P GAIN WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        36.69        59.24        31.56        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        12.49        11.47        66.05        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BM 
       17.79        21.63        16.18        66.31        21.30        35.67 
TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
       26.33         0.46         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
        4.14        23.97         0.10         9.80        21.37         8.94 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38         7.13        37.12        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
       36.39         5.26         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
       15.65         0.10        75.52         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       18.08         7.76         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.18        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
        0.72         6.58         5.06        13.22        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
       72.72        41.49        65.46        22.62        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.08         8.52        15.65         8.81        32.75        10.82 
TCGA-X9-A971 
       12.36 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.07               0.07 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             80.48             175.04 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              14.5               19.3 
[1] "0.1 - 80.5 (14.5)"  "0.1 - 175.0 (19.3)"
[1] "hr=" "2"  
D36V2, continuous
D36V3, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   21 19
  20P GAIN WILD-TYPE 67 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     21   19
  20P GAIN WILD-TYPE   67   49
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               21                 67
  MALE                 19                 49
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       2                         1    29
  20P GAIN WILD-TYPE     3                         9    86
D36V4, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   29                 86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = 20Q GAIN MUTATION ANALYSIS
D37V1, survival
                    sevent
clus2                 0  1
  20Q GAIN MUTATED   32 21
  20Q GAIN WILD-TYPE 72 30
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                53                102 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                 30 
$`20Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        18.54        46.68 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LW TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A48P 
       74.66         6.28       108.13        42.77        10.68        14.96 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       23.44         3.06        23.54        21.30        33.07        35.67 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G 
       26.33        19.43         1.15         0.10        20.32         0.07 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK 
        4.57        12.62        80.48         8.94         3.22        31.76 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I 
      143.41        13.58         5.92        27.29        11.70         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5V9 
        3.88         2.37         4.08        37.55         5.03        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B 
       18.08        21.01        93.40         3.88         6.58         5.06 
TCGA-UE-A6QU TCGA-WK-A8XX TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 
        0.72        38.27        27.16         8.35        24.62 

$`20Q GAIN WILD-TYPE`
TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       36.69        59.24        31.56        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        23.08        70.49        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       12.26        27.22        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        66.05        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A2OT 
       16.18        66.31         0.46         0.07         0.07        26.89 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.14        23.97         0.10        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38         7.13        37.12        25.22        28.21       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       36.39         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        0.10        75.52         6.35        38.63        81.01        18.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VG 
        7.76         1.84        48.59        18.18       175.04        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       10.52         0.72        13.22        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       41.49        65.46        22.62        50.89        17.26        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
        8.52        15.65         8.81        32.75        10.82        12.36 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.07               0.07 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            143.41             175.04 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            14.960             19.675 
[1] "0.1 - 143.4 (15.0)" "0.1 - 175.0 (19.7)"
[1] "hr=" "1.6"
D37V2, continuous
D37V3, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   27 26
  20Q GAIN WILD-TYPE 61 42
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     27   26
  20Q GAIN WILD-TYPE   61   42
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               27                 61
  MALE                 26                 42
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       2                         1    42
  20Q GAIN WILD-TYPE     3                         9    73
D37V4, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   42                 73
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = 21Q GAIN MUTATION ANALYSIS
D38V1, survival
                    sevent
clus2                 0  1
  21Q GAIN MUTATED   18 16
  21Q GAIN WILD-TYPE 86 35
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                34                121 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                16                 35 
$`21Q GAIN MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U9 
        2.04        12.85        46.68         8.58       108.13        14.99 
TCGA-DX-A48K TCGA-DX-A6YU TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
       19.30        23.54         4.57         0.10        41.33        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF 
        3.22         7.13        25.22        13.58         5.92         1.05 
TCGA-LI-A67I TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QC-A7B5 
        5.26         4.47         4.08        37.55         6.35         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-UE-A6QT 
        7.76        46.82        48.59        18.18        93.40        13.22 
TCGA-UE-A6QU TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X9-A971 
        0.72        38.27        22.62        12.36 

$`21Q GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        38.24        36.69        18.54        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       16.18         3.06        66.31        21.30        33.07        35.67 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       26.33        19.43         1.15         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
       20.32         0.07         0.07        26.89         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
       23.97         9.80        21.37         8.94         1.38        37.12 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       31.76        28.21       143.41       116.88        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W 
        6.28         3.91        71.70        36.39        27.29        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
        3.88         2.37         0.49         5.69        11.08        15.65 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
        0.10        75.52        38.63        81.01        18.08         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       18.08        21.01       175.04        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        3.88         6.58         5.06        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       41.49        65.46        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
        8.52        15.65         8.35         8.81        32.75        24.62 
TCGA-X6-A8C7 
       10.82 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.10               0.07 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            108.13             175.04 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
            13.035             20.320 
[1] "0.1 - 108.1 (13.0)" "0.1 - 175.0 (20.3)"
[1] "hr=" "1.9"
D38V2, continuous
D38V3, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED   18 16
  21Q GAIN WILD-TYPE 70 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     18   16
  21Q GAIN WILD-TYPE   70   52
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE               18                 70
  MALE                 16                 52
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       2                         4    22
  21Q GAIN WILD-TYPE     3                         6    93
D38V4, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                4                  6
  WHITE                                   22                 93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                 0  1
  22Q GAIN MUTATED   25 11
  22Q GAIN WILD-TYPE 79 40
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                36                119 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                11                 40 
$`22Q GAIN MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A3UA TCGA-DX-A48K TCGA-DX-A48O 
       14.04        38.24        12.85        10.68        19.30        27.22 
TCGA-DX-A48P TCGA-DX-A6BB TCGA-DX-A6BF TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
       14.96        23.44         2.07        26.89         4.14        12.62 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-JV-A5VE TCGA-JV-A75J 
       41.33         8.94         3.22        31.76         6.28         3.91 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
        3.88         2.37         4.47         4.08        37.55         6.35 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF 
       18.08         5.03        46.82        48.59        18.18        93.40 
TCGA-SG-A849 TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 
        6.58        22.62        17.26         8.35         8.81        24.62 

$`22Q GAIN WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
        2.04        36.69        18.54        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       12.26        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       66.05        28.96        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       66.31        23.54        21.30        33.07        35.67        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       19.43         1.15         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        0.07         0.07         4.57        23.97         0.10         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         1.38         7.13        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W 
       22.62         1.05        71.70        36.39        27.29        11.70 
TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        5.26         0.49         5.69        11.08        15.65         0.10 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       75.52        38.63        81.01         7.76         1.84        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
       21.01       175.04        55.50        10.52         0.72         3.88 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
        5.06        13.22         0.72        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WC 
       41.49        38.27        65.46        50.89        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
        8.52        15.65        32.75        10.82        12.36 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              2.07               0.07 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             93.40             175.04 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
            13.445             21.010 
[1] "2.1 - 93.4 (13.4)"  "0.1 - 175.0 (21.0)"
[1] "hr=" "1.3"
D39V2, continuous
D39V3, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED   24 12
  22Q GAIN WILD-TYPE 64 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED     24   12
  22Q GAIN WILD-TYPE   64   56
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE               24                 64
  MALE                 12                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       1                         4    28
  22Q GAIN WILD-TYPE     4                         6    87
D39V4, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                4                  6
  WHITE                                   28                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                0  1
  XQ GAIN MUTATED   11  8
  XQ GAIN WILD-TYPE 93 43
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               19               136 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                8                43 
$`XQ GAIN MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A6YS TCGA-DX-A8BX TCGA-HB-A2OT 
       36.69         6.28        60.30        66.31        19.43        26.89 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W 
       41.33        80.48         8.94        13.58         3.91        27.29 
TCGA-LI-A67I TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SG-A849 
        5.26        18.08        93.40        10.52         3.88         6.58 
TCGA-WK-A8XS 
       72.72 

$`XQ GAIN WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       15.06        17.75        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-AATS 
       23.54        21.30        33.07        35.67        26.33         1.15 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
       31.76        28.21       143.41       116.88        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       22.62         6.28         1.05        71.70        36.39        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        3.88         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        81.01        18.08         5.03         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VG 
       46.82        48.59        18.18        21.01       175.04        55.50 
TCGA-RN-A68Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        0.72         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46        22.62        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       18.08        27.16         8.52        15.65         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             3.88              0.07 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            93.40            175.04 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            19.43             18.13 
[1] "3.9 - 93.4 (19.4)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.1"
D40V2, continuous
D40V3, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   12  7
  XQ GAIN WILD-TYPE 76 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     12    7
  XQ GAIN WILD-TYPE   76   61
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              12                76
  MALE                 7                61
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    14
  XQ GAIN WILD-TYPE     5                         9   101
D40V4, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  14               101
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = 1P LOSS MUTATION ANALYSIS
D41V1, survival
                   sevent
clus2                0  1
  1P LOSS MUTATED   17  5
  1P LOSS WILD-TYPE 87 46
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               22               133 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                5                46 
$`1P LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A6B9 
       38.24        36.69        18.54        10.68        64.18        11.47 
TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A7EF TCGA-FX-A3RE TCGA-FX-A48G TCGA-IE-A6BZ 
       66.05        66.31        21.30         0.07         0.07         7.13 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-MO-A47R TCGA-QQ-A8VB 
      143.41       116.88        73.28        22.62         0.10       175.04 
TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-X6-A7WD TCGA-X9-A971 
       41.49        22.62         8.52        12.36 

$`1P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        28.80        34.88         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       12.49        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       16.18         3.06        23.54        33.07        35.67        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y 
       19.43         1.15         0.46         0.10        20.32         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3KA 
        1.38        37.12        25.22        31.76        28.21        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92         6.28         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA 
       27.29        11.70         5.26         3.88         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69         4.47        11.08        15.65         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
       37.55         6.35        38.63        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        7.76         1.84        46.82        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
       21.01        93.40        55.50        10.52         0.72         3.88 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        6.58         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       72.72        38.27        65.46        50.89        17.26        18.08 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       27.16        15.65         8.35         8.81        32.75        24.62 
TCGA-X6-A8C7 
       10.82 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.07              0.07 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           175.04            108.13 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            22.62             18.08 
[1] "0.1 - 175.0 (22.6)" "0.1 - 108.1 (18.1)"
[1] "hr=" "2.3"
D41V2, continuous
D41V3, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   19  3
  1P LOSS WILD-TYPE 69 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     19    3
  1P LOSS WILD-TYPE   69   65
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              19                69
  MALE                 3                65
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       2                         1    16
  1P LOSS WILD-TYPE     3                         9    99
D41V4, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  16                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = 1Q LOSS MUTATION ANALYSIS
D42V1, survival
                   sevent
clus2                0  1
  1Q LOSS MUTATED   15  7
  1Q LOSS WILD-TYPE 89 44
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               22               133 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                7                44 
$`1Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A6BA TCGA-DX-A6BF 
       38.24        36.69        18.54         9.70        66.05         2.07 
TCGA-DX-A6YS TCGA-DX-A7EF TCGA-FX-A2QS TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A5W3 
       66.31        21.30         0.46         0.07         4.57        12.62 
TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-LI-A9QH TCGA-N1-A6IA TCGA-PC-A5DO 
        7.13       143.41       116.88         3.88         4.08        81.01 
TCGA-QC-AA9N TCGA-SI-AA8B TCGA-WK-A8Y0 TCGA-X6-A7WD 
        7.76         5.06        22.62         8.52 

$`1Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        12.85        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       23.08        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       24.26        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       25.08        12.49        11.47        23.44        28.96        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM 
       21.63        16.18         3.06        23.54        33.07        35.67 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       26.33        19.43         1.15         0.10         0.07        20.32 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.07        26.89         4.14        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        25.22        31.76        28.21        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       36.39        27.29        11.70         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DK 
        5.69         4.47        11.08        15.65         0.10        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 
       37.55         6.35        38.63        18.08         5.03         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        18.18        21.01       175.04 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 
       93.40        55.50        10.52         0.72         3.88         6.58 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       13.22         0.72        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        50.89        17.26        18.08        27.16 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       15.65         8.35         8.81        32.75        24.62        10.82 
TCGA-X9-A971 
       12.36 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.07              0.07 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           143.41            175.04 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            11.16             19.30 
[1] "0.1 - 143.4 (11.2)" "0.1 - 175.0 (19.3)"
[1] "hr=" "1.1"
D42V2, continuous
D42V3, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED   17  5
  1Q LOSS WILD-TYPE 71 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     17    5
  1Q LOSS WILD-TYPE   71   63
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE              17                71
  MALE                 5                63
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         2    16
  1Q LOSS WILD-TYPE     5                         8    99
D42V4, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  16                99
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = 2P LOSS MUTATION ANALYSIS
D43V1, survival
                   sevent
clus2                0  1
  2P LOSS MUTATED   31 18
  2P LOSS WILD-TYPE 73 33
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               49               106 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               18                33 
$`2P LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC 
       18.54        59.24         6.28        42.77        14.99        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48R 
       28.80        34.88        64.18        24.26        14.96        26.47 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO 
       25.08        66.05         3.06        23.54        35.67        26.33 
TCGA-DX-AATS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        1.15        20.32        26.89         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
        0.10         9.80        80.48         3.22         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-LI-A9QH 
       25.22        31.76         6.28        71.70        27.29         3.88 
TCGA-MJ-A68H TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-SI-AA8B 
        4.47        81.01        18.08         7.76        46.82         5.06 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WB TCGA-X6-A8C2 
       72.72        38.27        65.46        22.62        18.08        15.65 
TCGA-X9-A971 
       12.36 

$`2P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        36.69        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J 
       15.06        17.75         4.54        10.68        44.45         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       19.30        12.26        27.22        72.72        12.49        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ 
       66.31        21.30        33.07        19.43         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A4EH 
        0.07         0.07         0.07         4.57        41.33        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
        8.94         1.38        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
       73.28         5.92        22.62         1.05         3.91        36.39 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       11.70         5.26         2.37         0.49         5.69        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       38.63         5.03         1.84        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        3.88         6.58        13.22         0.72        11.93         4.80 
TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       41.49        50.89        17.26        27.16         8.52         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.81        32.75        24.62        10.82 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             0.10              0.07 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            81.01            175.04 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            23.97             17.18 
[1] "0.1 - 81.0 (24.0)"  "0.1 - 175.0 (17.2)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                   cls
clus                 0  1
  2P LOSS MUTATED   33 16
  2P LOSS WILD-TYPE 55 52
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED     33   16
  2P LOSS WILD-TYPE   55   52
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE              33                55
  MALE                16                52
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         4    38
  2P LOSS WILD-TYPE     5                         6    77
D43V4, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               4                 6
  WHITE                                  38                77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = 2Q LOSS MUTATION ANALYSIS
D44V1, survival
                   sevent
clus2                0  1
  2Q LOSS MUTATED   23 17
  2Q LOSS WILD-TYPE 81 34
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               40               115 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
               17                34 
$`2Q LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD 
       18.54        59.24         6.28        42.77        14.99        28.80 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A8BL 
       24.26        26.47        25.08        16.18         3.06        33.07 
TCGA-DX-AATS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        1.15        20.32        26.89         4.57         4.14        12.62 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
        0.10         9.80         3.22         7.13        37.12        31.76 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP 
        6.28         1.05        27.29         4.47         6.35        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX 
        5.03         7.76         3.88         5.06        72.72        38.27 
TCGA-WK-A8Y0 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
       22.62        18.08        27.16        15.65 

$`2Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        36.69        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        72.72        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YU 
       28.96         2.07        17.79        21.63        66.31        23.54 
TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ 
       21.30        35.67        26.33        19.43         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV 
        0.07         0.07         0.07        23.97        41.33        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37         8.94         1.38        25.22        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       71.70        36.39        11.70         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       75.52        37.55        38.63        81.01         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       18.08        48.59        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       55.50        10.52         0.72         6.58        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
       11.93         4.80        41.49        65.46        50.89        17.26 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.52         8.35         8.81        32.75        24.62        10.82 
TCGA-X9-A971 
       12.36 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
             0.10              0.07 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            72.72            175.04 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           15.915            20.050 
[1] "0.1 - 72.7 (15.9)"  "0.1 - 175.0 (20.1)"
[1] "hr=" "2.3"
D44V2, continuous
D44V3, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED   23 17
  2Q LOSS WILD-TYPE 65 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED     23   17
  2Q LOSS WILD-TYPE   65   51
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE              23                65
  MALE                17                51
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         5    29
  2Q LOSS WILD-TYPE     5                         5    86
D44V4, multiclass
                           clus
vv                          2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               5                 5
  WHITE                                  29                86
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                0  1
  3P LOSS MUTATED   18 14
  3P LOSS WILD-TYPE 86 37
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               32               123 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               14                37 
$`3P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS 
        2.04        38.24        18.54        74.66         6.28         9.04 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48R 
       23.08        17.10        20.05        10.68        12.26        26.47 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-AATS TCGA-HB-A3YV 
        3.06        23.54        21.30        35.67         1.15         4.57 
TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-LI-A9QH 
        4.14         3.22         7.13        37.12         1.05         3.88 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-WK-A8XT TCGA-X6-A8C4 
        0.10        37.55         6.35       175.04        41.49         8.81 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

$`3P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        36.69        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58         9.70        59.47        54.77        70.49       108.13 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       24.26        27.22        14.96        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BX 
       21.63        16.18        66.31        33.07        26.33        19.43 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       26.89        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         8.94         1.38        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62         6.28         3.91        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       11.70         5.26         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       11.08        15.65         4.08        75.52        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        18.18        21.01        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
        0.72         3.88         6.58         5.06        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        72.72        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       50.89        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 
        8.35        32.75        24.62 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.10              0.07 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
           175.04            143.41 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            11.54             20.32 
[1] "0.1 - 175.0 (11.5)" "0.1 - 143.4 (20.3)"
[1] "hr=" "2.1"
D45V2, continuous
D45V3, binary
                   cls
clus                 0  1
  3P LOSS MUTATED   19 14
  3P LOSS WILD-TYPE 69 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     19   14
  3P LOSS WILD-TYPE   69   54
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE              19                69
  MALE                14                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         1    25
  3P LOSS WILD-TYPE     4                         9    90
D45V4, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  25                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                0  1
  3Q LOSS MUTATED   16 15
  3Q LOSS WILD-TYPE 88 36
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               31               124 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               15                36 
$`3Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y 
        2.04        38.24        18.54        46.68        74.66         6.28 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48N 
        9.04        23.08        17.10        20.05        10.68        12.26 
TCGA-DX-A48R TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-AATS TCGA-HB-A3YV TCGA-HB-A43Z 
       26.47         3.06        21.30         1.15         4.57         4.14 
TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-LI-A9QH 
       80.48         3.22         7.13        37.12         1.05         3.88 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A8VB TCGA-X6-A8C4 
        4.47         0.10        37.55         6.35       175.04         8.81 
TCGA-X9-A971 
       12.36 

$`3Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        36.69        59.24        31.56        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
        9.70        59.47        54.77        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        14.99        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       27.22        14.96        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       16.18        66.31        23.54        33.07        35.67        26.33 
TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       19.43         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.07        26.89        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
        9.80        21.37         8.94         1.38        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62         6.28         3.91        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J 
       11.70         5.26         2.37         0.49         5.69        11.08 
TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       15.65         4.08        75.52        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         7.76         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       18.18        21.01        93.40        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       50.89        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
        8.35        32.75        24.62        10.82 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             0.10              0.07 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           175.04            143.41 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
           10.680            20.665 
[1] "0.1 - 175.0 (10.7)" "0.1 - 143.4 (20.7)"
[1] "hr=" "2.2"
D46V2, continuous
D46V3, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED   17 14
  3Q LOSS WILD-TYPE 71 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED     17   14
  3Q LOSS WILD-TYPE   71   54
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE              17                71
  MALE                14                54
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         2    21
  3Q LOSS WILD-TYPE     4                         8    94
D46V4, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  21                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   14 10
  4P LOSS WILD-TYPE 90 41
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               24               131 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               10                41 
$`4P LOSS MUTATED`
TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UD 
        8.58         9.04        23.08        42.77        10.68        28.80 
TCGA-DX-A3UE TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6YS TCGA-DX-A7EF TCGA-HB-A43Z 
       34.88        24.26        26.47        66.31        21.30         4.14 
TCGA-HB-A5W3 TCGA-IE-A4EK TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42W 
       12.62         1.38         5.92        22.62         1.05        27.29 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MO-A47R TCGA-PC-A5DM TCGA-QQ-A5V9 TCGA-X2-A95T 
        5.26         3.88         0.10         6.35        46.82        50.89 

$`4P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       76.41        66.87         6.28        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       59.47        54.77        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75         4.54        14.99        44.45        39.35 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS 
       23.54        33.07        35.67        26.33        19.43         1.15 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       26.89         4.57        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        21.37         8.94         3.22         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W 
       73.28         6.28         3.91        71.70        36.39        11.70 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52        37.55        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         7.76         1.84        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       17.26        18.08        27.16         8.52        15.65         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        32.75        24.62        10.82        12.36 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.10              0.07 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            66.31            175.04 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            16.96             18.18 
[1] "0.1 - 66.3 (17.0)"  "0.1 - 175.0 (18.2)"
[1] "hr=" "1.8"
D47V2, continuous
D47V3, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   15  9
  4P LOSS WILD-TYPE 73 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     15    9
  4P LOSS WILD-TYPE   73   59
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              15                73
  MALE                 9                59
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       2                         1    20
  4P LOSS WILD-TYPE     3                         9    95
D47V4, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = 4Q LOSS MUTATION ANALYSIS
D48V1, survival
                   sevent
clus2                0  1
  4Q LOSS MUTATED   23  9
  4Q LOSS WILD-TYPE 81 42
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               32               123 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                9                42 
$`4Q LOSS MUTATED`
TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UA 
       74.66         8.58         9.04        23.08        42.77        10.68 
TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YS 
       28.80        24.26        26.47        66.05         3.06        66.31 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BM TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EH 
       23.54        21.30        35.67         4.14         0.10        21.37 
TCGA-IE-A4EK TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42W TCGA-KF-A41W 
        1.38         5.92        22.62         1.05        27.29        11.70 
TCGA-LI-A67I TCGA-MO-A47R TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-WK-A8XS 
        5.26         0.10         6.35         7.76        46.82        72.72 
TCGA-X6-A7WD TCGA-X6-A8C4 
        8.52         8.81 

$`4Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        59.24        31.56        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       54.77        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       17.75         4.54        14.99        44.45        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        12.49        11.47        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A8BL TCGA-DX-A8BO 
        2.07        17.79        21.63        16.18        33.07        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       19.43         1.15         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         0.07        26.89         4.57        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       41.33         9.80        80.48         8.94         3.22         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28         6.28         3.91        71.70        36.39 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        3.88         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
       15.65         4.08        75.52        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       18.08         5.03         1.84        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
        4.80        41.49        38.27        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       17.26        18.08        27.16        15.65         8.35        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       24.62        10.82        12.36 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.10              0.07 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            74.66            175.04 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            16.50             18.18 
[1] "0.1 - 74.7 (16.5)"  "0.1 - 175.0 (18.2)"
[1] "hr=" "1"  
D48V2, continuous
D48V3, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   22 10
  4Q LOSS WILD-TYPE 66 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     22   10
  4Q LOSS WILD-TYPE   66   58
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              22                66
  MALE                10                58
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       2                         2    24
  4Q LOSS WILD-TYPE     3                         8    91
D48V4, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  24                91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = 5P LOSS MUTATION ANALYSIS
D49V1, survival
                   sevent
clus2                0  1
  5P LOSS MUTATED    9  5
  5P LOSS WILD-TYPE 95 46
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               14               141 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                5                46 
$`5P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA 
        2.04        36.69        74.66        23.08        20.05        10.68 
TCGA-DX-A6YQ TCGA-DX-A8BO TCGA-IS-A3K7 TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-WK-A8Y0 
        3.06        26.33       143.41         5.69        48.59        22.62 
TCGA-X6-A8C3 TCGA-X6-A8C6 
        8.35        24.62 

$`5P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        38.24        12.85        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL 
       21.63        16.18        66.31        23.54        21.30        33.07 
TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       35.67        19.43         1.15         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       20.32         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        31.76        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       36.39        27.29        11.70         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         4.47        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
       75.52        37.55         6.35        38.63        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC 
        5.03         7.76         1.84        46.82        18.08        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       21.01       175.04        93.40        55.50        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        3.88         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
        4.80        72.72        41.49        38.27        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 
       17.26        18.08        27.16         8.52        15.65         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        10.82        12.36 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             2.04              0.07 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           143.41            175.04 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            22.85             18.08 
[1] "2.0 - 143.4 (22.9)" "0.1 - 175.0 (18.1)"
[1] "hr=" "1"  
D49V2, continuous
D49V3, binary
                   cls
clus                 0  1
  5P LOSS MUTATED    9  5
  5P LOSS WILD-TYPE 79 63
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      9    5
  5P LOSS WILD-TYPE   79   63
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE               9                79
  MALE                 5                63
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       1                         0     9
  5P LOSS WILD-TYPE     4                        10   106
D49V4, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                10
  WHITE                                   9               106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = 5Q LOSS MUTATION ANALYSIS
D50V1, survival
                   sevent
clus2                0  1
  5Q LOSS MUTATED   14  7
  5Q LOSS WILD-TYPE 90 44
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               21               134 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                7                44 
$`5Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA 
        2.04        36.69        74.66        23.08        20.05        10.68 
TCGA-DX-A7EF TCGA-DX-A8BO TCGA-DX-AATS TCGA-FX-A2QS TCGA-IE-A4EH TCGA-IE-A6BZ 
       21.30        26.33         1.15         0.46        21.37         7.13 
TCGA-IF-A4AJ TCGA-LI-A9QH TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-WK-A8Y0 TCGA-X6-A7WC 
       25.22         3.88         5.69        48.59        22.62        27.16 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C6 
        8.52         8.35        24.62 

$`5Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        38.24        12.85        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL 
       21.63        16.18         3.06        66.31        23.54        33.07 
TCGA-DX-A8BM TCGA-DX-A8BX TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       35.67        19.43         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33         9.80        80.48         8.94         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38        37.12        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I 
        3.91        71.70        36.39        27.29        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        2.37         0.49         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.18        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU 
        0.72         3.88         6.58         5.06        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       50.89        17.26        18.08        15.65         8.81        32.75 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             0.46              0.07 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            74.66            175.04 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            21.30             18.08 
[1] "0.5 - 74.7 (21.3)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.4"
D50V2, continuous
D50V3, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   13  8
  5Q LOSS WILD-TYPE 75 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     13    8
  5Q LOSS WILD-TYPE   75   60
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              13                75
  MALE                 8                60
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       1                         0    17
  5Q LOSS WILD-TYPE     4                        10    98
D50V4, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                10
  WHITE                                  17                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"

Clustering(51) Variable = 6P LOSS MUTATION ANALYSIS
D51V1, survival
                   sevent
clus2                0  1
  6P LOSS MUTATED   30  8
  6P LOSS WILD-TYPE 74 43
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               38               117 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                8                43 
$`6P LOSS MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA 
       36.69        74.66        23.08        17.10        20.05        10.68 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       39.35        64.18        19.30        24.26        27.22        14.96 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YS 
       25.08        66.05        23.44         2.07        16.18        66.31 
TCGA-DX-A8BL TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A3OV TCGA-IW-A3M6 
       33.07         0.07         4.14        12.62        80.48        22.62 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-MB-A8JL TCGA-PC-A5DL TCGA-QC-A7B5 TCGA-QQ-A5VD 
       71.70        36.39         5.69        37.55         5.03        21.01 
TCGA-QQ-A8VB TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X6-A7WC TCGA-X6-A8C3 
      175.04        11.93        72.72        65.46        27.16         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 
        8.81        32.75 

$`6P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        31.56        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 
       54.77         9.04        70.49       108.13        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       42.77         4.54        14.99        44.45        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
        9.73        12.26        26.47        72.72        12.49        11.47 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A7EF 
       28.96        17.79        21.63         3.06        23.54        21.30 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ 
       35.67        26.33        19.43         1.15         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 
        0.07        20.32         0.07        26.89         4.57        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.10        41.33         9.80        21.37         8.94         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38         7.13        37.12        25.22        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28         5.92         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        1.05         3.91        27.29        11.70         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        2.37         0.49         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        4.08        75.52         6.35        38.63        81.01        18.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        7.76         1.84        46.82        18.08        48.59        18.18 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 
       93.40        55.50        10.52         0.72         3.88         6.58 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        5.06        13.22         0.72         4.80        41.49        38.27 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       22.62        50.89        17.26        18.08         8.52        15.65 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       24.62        10.82        12.36 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             0.07              0.07 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
           175.04            143.41 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            23.85             17.26 
[1] "0.1 - 175.0 (23.9)" "0.1 - 143.4 (17.3)"
[1] "hr=" "2.2"
D51V2, continuous
D51V3, binary
                   cls
clus                 0  1
  6P LOSS MUTATED   23 15
  6P LOSS WILD-TYPE 65 53
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED     23   15
  6P LOSS WILD-TYPE   65   53
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE              23                65
  MALE                15                53
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       2                         1    33
  6P LOSS WILD-TYPE     3                         9    82
D51V4, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  33                82
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = 6Q LOSS MUTATION ANALYSIS
D52V1, survival
                   sevent
clus2                0  1
  6Q LOSS MUTATED   21 10
  6Q LOSS WILD-TYPE 83 41
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               31               124 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               10                41 
$`6Q LOSS MUTATED`
TCGA-DX-A23R TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P 
       74.66        42.77        10.68        64.18        24.26        14.96 
TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-FX-A3TO 
       25.08        66.05        66.31        21.30        33.07        20.32 
TCGA-FX-A48G TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-MB-A8JL TCGA-PC-A5DO 
        0.07         4.14         0.10        80.48         5.69        81.01 
TCGA-QC-A7B5 TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z7 
        5.03        21.01       175.04        93.40        10.52         3.88 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C3 
       11.93        72.72        65.46        22.62        27.16         8.35 
TCGA-X6-A8C5 
       32.75 

$`6Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        59.24        31.56        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       12.26        27.22        26.47        72.72        12.49        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS 
        3.06        23.54        35.67        26.33        19.43         1.15 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.46         0.10         0.07         0.07        26.89         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62        23.97        41.33         9.80        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        3.22         1.38         7.13        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62         6.28         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA 
       27.29        11.70         5.26         3.88         2.37         0.49 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        4.47        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55         6.35        38.63        18.08         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VG TCGA-RN-A68Q 
       46.82        18.08        48.59        18.18        55.50         0.72 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT 
        6.58         5.06        13.22         0.72         4.80        41.49 
TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       38.27        50.89        17.26        18.08         8.52        15.65 
TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        24.62        10.82        12.36 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.07              0.07 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
           175.04            143.41 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            24.26             17.77 
[1] "0.1 - 175.0 (24.3)" "0.1 - 143.4 (17.8)"
[1] "hr=" "1.5"
D52V2, continuous
D52V3, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED   21 10
  6Q LOSS WILD-TYPE 67 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     21   10
  6Q LOSS WILD-TYPE   67   58
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE              21                67
  MALE                10                58
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         1    27
  6Q LOSS WILD-TYPE     4                         9    88
D52V4, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  27                88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = 7P LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                0  1
  7P LOSS MUTATED   17  6
  7P LOSS WILD-TYPE 87 45
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
               23               132 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
                6                45 
$`7P LOSS MUTATED`
TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48P TCGA-DX-A48U 
        6.28        17.10        42.77        28.80        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A7EF TCGA-FX-A3TO TCGA-HS-A5N7 
       25.08         2.07        21.63        21.30        20.32        23.97 
TCGA-IE-A3OV TCGA-IW-A3M6 TCGA-K1-A42W TCGA-KF-A41W TCGA-MB-A5YA TCGA-PC-A5DM 
       80.48        22.62        27.29        11.70         0.49         6.35 
TCGA-PC-A5DO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A8C6 TCGA-X9-A971 
       81.01        72.72        38.27        24.62        12.36 

$`7P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B9 
       24.26        12.26        27.22        26.47        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A6YQ 
       66.05        23.44        28.96        17.79        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX 
       66.31        23.54        33.07        35.67        26.33        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
        1.15         0.46         0.10         0.07         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 
       26.89         4.57         4.14        12.62         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
        9.80        21.37         8.94         3.22         1.38         7.13 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92         6.28         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JL 
       71.70        36.39         5.26         3.88         2.37         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        4.47        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        18.08         5.03         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
       46.82        18.08        48.59        18.18        21.01       175.04 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 
       93.40        55.50        10.52         0.72         3.88         6.58 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        5.06        13.22         0.72        11.93         4.80        41.49 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46        22.62        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
        8.52        15.65         8.35         8.81        32.75        10.82 

  7P LOSS MUTATED 7P LOSS WILD-TYPE 
             0.49              0.07 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
            81.01            175.04 
  7P LOSS MUTATED 7P LOSS WILD-TYPE 
           22.620            17.935 
[1] "0.5 - 81.0 (22.6)"  "0.1 - 175.0 (17.9)"
[1] "hr=" "1.6"
D53V2, continuous
D53V3, binary
                   cls
clus                 0  1
  7P LOSS MUTATED   10 13
  7P LOSS WILD-TYPE 78 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P LOSS MUTATED     10   13
  7P LOSS WILD-TYPE   78   55
        clus
vv       7P LOSS MUTATED 7P LOSS WILD-TYPE
  FEMALE              10                78
  MALE                13                55
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P LOSS MUTATED       1                         0    20
  7P LOSS WILD-TYPE     4                        10    95
D53V4, multiclass
                           clus
vv                          7P LOSS MUTATED 7P LOSS WILD-TYPE
  ASIAN                                   1                 4
  BLACK OR AFRICAN AMERICAN               0                10
  WHITE                                  20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = 7Q LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  7Q LOSS MUTATED   12  9
  7Q LOSS WILD-TYPE 92 42
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
               21               134 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                9                42 
$`7Q LOSS MUTATED`
TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48P TCGA-DX-A6BF 
       17.10        42.77        28.80         9.73        14.96         2.07 
TCGA-DX-A6BH TCGA-DX-A6YU TCGA-FX-A3TO TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IW-A3M5 
       21.63        23.54        20.32        37.12        25.22         5.92 
TCGA-K1-A42W TCGA-MB-A5YA TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QQ-A5VA TCGA-QQ-A8VH 
       27.29         0.49         6.35        18.08        18.08        10.52 
TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX 
        5.06        72.72        38.27 

$`7Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
      108.13        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K 
       10.68        44.45        39.35        34.88        64.18        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       12.49        11.47        66.05        23.44        28.96        17.79 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       16.18         3.06        66.31        21.30        33.07        35.67 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       26.33        19.43         1.15         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07        26.89         4.57         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 
        8.94         3.22         1.38         7.13        31.76        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        11.70         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        3.88         2.37         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        0.10         4.08        75.52        37.55        38.63        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         7.76         1.84        46.82        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 
       21.01       175.04        93.40        55.50         0.72         3.88 
TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        6.58        13.22         0.72        11.93         4.80        41.49 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       65.46        22.62        50.89        17.26        18.08        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
        8.52        15.65         8.35         8.81        32.75        24.62 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
             0.49              0.07 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            72.72            175.04 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            18.08             18.36 
[1] "0.5 - 72.7 (18.1)"  "0.1 - 175.0 (18.4)"
[1] "hr=" "1.7"
D54V2, continuous
D54V3, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED   11 10
  7Q LOSS WILD-TYPE 77 58
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED     11   10
  7Q LOSS WILD-TYPE   77   58
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE              11                77
  MALE                10                58
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         1    20
  7Q LOSS WILD-TYPE     5                         9    95
D54V4, multiclass
                           clus
vv                          7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               1                 9
  WHITE                                  20                95
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = 8P LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   23 10
  8P LOSS WILD-TYPE 81 41
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               33               122 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               10                41 
$`8P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS 
        2.04        38.24        36.69        59.24         6.28         9.04 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R 
       42.77        10.68        44.45         9.73        19.30        26.47 
TCGA-DX-A6BK TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3RE 
       16.18        21.30        33.07         1.15         0.46         0.07 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VE 
        4.14         0.10        41.33         7.13       143.41         6.28 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JL TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-WK-A8XS 
       11.70         3.88         5.69        48.59         3.88        72.72 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X9-A971 
       15.65         8.81        12.36 

$`8P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        18.54        46.68        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58         9.70        59.47        54.77        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
      108.13        17.10        20.05        15.06        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L 
       14.99        39.35        28.80        34.88        64.18        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       12.26        27.22        14.96        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO 
       21.63         3.06        66.31        23.54        35.67        26.33 
TCGA-DX-A8BX TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
       19.43         0.10        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        4.57        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        8.94         3.22         1.38        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I 
        1.05         3.91        71.70        36.39        27.29         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        2.37         0.49         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.18        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        0.72         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
        4.80        41.49        38.27        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 
       17.26        18.08        27.16         8.52         8.35        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 
       24.62        10.82 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.07              0.07 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           143.41            175.04 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           11.700            20.185 
[1] "0.1 - 143.4 (11.7)" "0.1 - 175.0 (20.2)"
[1] "hr=" "1.1"
D55V2, continuous
D55V3, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   21 13
  8P LOSS WILD-TYPE 67 55
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     21   13
  8P LOSS WILD-TYPE   67   55
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              21                67
  MALE                13                55
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       0                         2    25
  8P LOSS WILD-TYPE     5                         8    90
D55V4, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               2                 8
  WHITE                                  25                90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = 8Q LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                0  1
  8Q LOSS MUTATED   18  8
  8Q LOSS WILD-TYPE 86 43
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               26               129 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                8                43 
$`8Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3U7 
       38.24        36.69        59.24         6.28         9.04        42.77 
TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-AATS 
        9.73        24.26         3.06        21.30        33.07         1.15 
TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-KF-A41W 
        4.14         3.22         7.13       143.41         6.28        11.70 
TCGA-LI-A9QH TCGA-PC-A5DO TCGA-QC-AA9N TCGA-SI-AA8B TCGA-WK-A8XS TCGA-X2-A95T 
        3.88        81.01         7.76         5.06        72.72        50.89 
TCGA-X6-A8C2 TCGA-X9-A971 
       15.65        12.36 

$`8Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04         2.04        12.85        18.54        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        59.47        54.77        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88        64.18        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         2.07        17.79        21.63        16.18 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-FX-A2QS 
       66.31        23.54        35.67        26.33        19.43         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         8.94         1.38        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       31.76        28.21       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62         1.05         3.91        71.70        36.39        27.29 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        5.26         2.37         0.49         5.69         4.47        11.08 
TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         0.10         4.08        75.52        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       38.63        18.08         5.03         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        18.18        21.01       175.04        93.40        55.50 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       10.52         0.72         3.88         6.58        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        41.49        38.27        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08        27.16         8.52         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             1.15              0.07 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
           143.41            175.04 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            12.03             19.30 
[1] "1.1 - 143.4 (12.0)" "0.1 - 175.0 (19.3)"
[1] "hr=" "1.1"
D56V2, continuous
D56V3, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED   18  9
  8Q LOSS WILD-TYPE 70 59
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     18    9
  8Q LOSS WILD-TYPE   70   59
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE              18                70
  MALE                 9                59
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         3    19
  8Q LOSS WILD-TYPE     5                         7    96
D56V4, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 5
  BLACK OR AFRICAN AMERICAN               3                 7
  WHITE                                  19                96
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = 9P LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                0  1
  9P LOSS MUTATED   33 17
  9P LOSS WILD-TYPE 71 34
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               50               105 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               17                34 
$`9P LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW 
       14.04        12.85        66.87         6.28         9.04       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J 
       17.10        20.05        42.77        28.80        64.18         9.73 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ 
       26.47        25.08        12.49        66.05         2.07         3.06 
TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT 
       66.31        21.30        26.33         0.46         0.07        26.89 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 
        0.10        80.48         8.94         3.22       143.41         5.92 
TCGA-JV-A75J TCGA-K1-A42W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R 
        3.91        27.29         3.88         2.37         5.69         0.10 
TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VC TCGA-QQ-A8VB 
        4.08        38.63        81.01         5.03        18.18       175.04 
TCGA-QQ-A8VH TCGA-UE-A6QU TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A8C3 
       10.52         0.72        38.27        65.46        22.62         8.35 
TCGA-X6-A8C4 TCGA-X9-A971 
        8.81        12.36 

$`9P LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        38.24        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z 
       31.56        42.54        74.66         5.26        76.41        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT 
       60.30         8.58         9.70        59.47        54.77        23.08 
TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       70.49        15.06        17.75         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       44.45        39.35        34.88        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       27.22        14.96        72.72        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM 
       17.79        21.63        16.18        23.54        33.07        35.67 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       19.43         1.15         0.10        20.32         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37         1.38         7.13        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       116.88        13.58        73.28        22.62         6.28 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5YA 
        1.05        71.70        36.39        11.70         5.26         0.49 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        4.47        11.08        15.65        75.52        37.55         6.35 
TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       18.08         7.76         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 
       21.01        93.40        55.50         0.72         3.88         6.58 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        5.06        13.22        11.93         4.80        72.72        41.49 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       50.89        17.26        18.08        27.16         8.52        15.65 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.07              0.07 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           175.04            116.88 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
           13.445            19.430 
[1] "0.1 - 175.0 (13.4)" "0.1 - 116.9 (19.4)"
[1] "hr=" "1"  
D57V2, continuous
D57V3, binary
                   cls
clus                 0  1
  9P LOSS MUTATED   33 17
  9P LOSS WILD-TYPE 55 51
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     33   17
  9P LOSS WILD-TYPE   55   51
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE              33                55
  MALE                17                51
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       3                         3    39
  9P LOSS WILD-TYPE     2                         7    76
D57V4, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   3                 2
  BLACK OR AFRICAN AMERICAN               3                 7
  WHITE                                  39                76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = 9Q LOSS MUTATION ANALYSIS
D58V1, survival
                   sevent
clus2                0  1
  9Q LOSS MUTATED   15 14
  9Q LOSS WILD-TYPE 89 37
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               29               126 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               14                37 
$`9Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3UD 
       14.04        12.85         6.28         9.04       108.13        28.80 
TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A7EF 
        9.73        26.47        25.08         2.07        66.31        21.30 
TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 
       26.89         0.10        80.48       143.41        13.58         5.92 
TCGA-JV-A75J TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DO TCGA-QQ-A8VB 
        3.91         5.69         4.47         0.10        81.01       175.04 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-UE-A6QU TCGA-WK-A8XX TCGA-X6-A8C4 
       10.52         3.88         0.72        38.27         8.81 

$`9Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
        2.04        38.24        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       34.88        64.18        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        72.72        12.49        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU 
       28.96        17.79        21.63        16.18         3.06        23.54 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
       33.07        35.67        26.33        19.43         1.15         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3YV 
        0.10         0.07        20.32         0.07         0.07         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        4.14        12.62        23.97        41.33         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
        8.94         3.22         1.38         7.13        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
       31.76        28.21       116.88        73.28        22.62         6.28 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I 
        1.05        71.70        36.39        27.29        11.70         5.26 
TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MJ-A850 TCGA-N1-A6IA 
        3.88         2.37         0.49        11.08        15.65         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 
       75.52        37.55         6.35        38.63        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        7.76         1.84        46.82        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B 
       21.01        93.40        55.50         0.72         6.58         5.06 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY 
       13.22        11.93         4.80        72.72        41.49        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       22.62        50.89        17.26        18.08        27.16         8.52 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       15.65         8.35        32.75        24.62        10.82        12.36 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.10              0.07 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           175.04            116.88 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
           12.850            19.365 
[1] "0.1 - 175.0 (12.8)" "0.1 - 116.9 (19.4)"
[1] "hr=" "1.6"
D58V2, continuous
D58V3, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED   18 11
  9Q LOSS WILD-TYPE 70 57
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     18   11
  9Q LOSS WILD-TYPE   70   57
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE              18                70
  MALE                11                57
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       2                         3    21
  9Q LOSS WILD-TYPE     3                         7    94
D58V4, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               3                 7
  WHITE                                  21                94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = 10P LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   53 20
  10P LOSS WILD-TYPE 51 31
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                73                 82 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                20                 31 
$`10P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3U9 
        2.04        38.24        18.54        74.66         6.28        14.99 
TCGA-DX-A3UA TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A48R 
       10.68        34.88        64.18        19.30        14.96        26.47 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK 
       12.49        11.47        66.05        23.44         2.07        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS TCGA-FX-A3RE 
        3.06        23.54        35.67        26.33         0.46         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       20.32         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       12.62        23.97         0.10        80.48         8.94         3.22 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        31.76       143.41         5.92        22.62         6.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5YA 
        3.91        71.70        27.29        11.70         3.88         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
        5.69         4.47         0.10         4.08        75.52        37.55 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01         5.03         7.76        46.82        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU 
       21.01       175.04        10.52         6.58         5.06         0.72 
TCGA-WK-A8XO TCGA-WK-A8XS TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 
       11.93        72.72        17.26         8.52         8.35        32.75 
TCGA-X9-A971 
       12.36 

$`10P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04        12.85        36.69        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J 
       42.77         4.54        44.45        39.35        28.80         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BE 
       24.26        12.26        27.22        72.72        25.08        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BX 
       17.79        21.63        66.31        21.30        33.07        19.43 
TCGA-DX-AATS TCGA-FX-A3NJ TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK 
        1.15         0.10        41.33         9.80        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        7.13        37.12        28.21       116.88        13.58        73.28 
TCGA-JV-A5VF TCGA-K1-A3PO TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MJ-A68J TCGA-MJ-A850 
        1.05        36.39         5.26         2.37        11.08        15.65 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VF 
        6.35        38.63        18.08         1.84        18.08        93.40 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XT 
       55.50         0.72         3.88        13.22         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        22.62        50.89        18.08        27.16 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 
       15.65         8.81        24.62        10.82 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.07               0.10 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            175.04             116.88 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            12.620             22.125 
[1] "0.1 - 175.0 (12.6)" "0.1 - 116.9 (22.1)"
[1] "hr=" "1.1"
D59V2, continuous
D59V3, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   53 20
  10P LOSS WILD-TYPE 35 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     53   20
  10P LOSS WILD-TYPE   35   48
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               53                 35
  MALE                 20                 48
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       4                         7    54
  10P LOSS WILD-TYPE     1                         3    61
D59V4, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    4                  1
  BLACK OR AFRICAN AMERICAN                7                  3
  WHITE                                   54                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = 10Q LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   57 27
  10Q LOSS WILD-TYPE 47 24
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                84                 71 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                27                 24 
$`10Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       38.24        18.54         6.28        42.77        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       39.35        34.88        64.18        19.30        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       14.96        26.47        72.72        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A8BO 
       23.44         2.07        16.18         3.06        23.54        26.33 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        0.10        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3KA 
        7.13        25.22        31.76        28.21       143.41        13.58 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W 
       22.62         6.28         1.05         3.91        71.70        27.29 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA 
       11.70         3.88         0.49         4.47         0.10         4.08 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V9 
       37.55         6.35        81.01        18.08         5.03        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A849 
       48.59        18.18        21.01       175.04        10.52         6.58 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA 
        5.06         0.72        72.72        65.46        22.62        17.26 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X9-A971 
       18.08         8.52        15.65         8.35        32.75        12.36 

$`10Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04         2.04        12.85        36.69        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J 
       15.06        17.75         4.54        44.45        28.80         9.73 
TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS 
       12.26        25.08        28.96        17.79        21.63        66.31 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-HS-A5N9 TCGA-HS-A5NA 
       21.30        33.07        35.67        19.43        41.33         9.80 
TCGA-IF-A3RQ TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-LI-A67I 
       37.12       116.88        73.28         5.92        36.39         5.26 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DN 
        2.37         5.69        11.08        15.65        75.52        38.63 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        7.76         1.84        18.08        93.40        55.50         0.72 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
        3.88        13.22        11.93         4.80        41.49        38.27 
TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 
       50.89        27.16         8.81        24.62        10.82 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.07               0.72 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            175.04             116.88 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            15.915             23.080 
[1] "0.1 - 175.0 (15.9)" "0.7 - 116.9 (23.1)"
[1] "hr=" "1.3"
D60V2, continuous
D60V3, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   60 24
  10Q LOSS WILD-TYPE 28 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     60   24
  10Q LOSS WILD-TYPE   28   44
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               60                 28
  MALE                 24                 44
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       4                         7    67
  10Q LOSS WILD-TYPE     1                         3    48
D60V4, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    4                  1
  BLACK OR AFRICAN AMERICAN                7                  3
  WHITE                                   67                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(61) Variable = 11P LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                 0  1
  11P LOSS MUTATED   39 21
  11P LOSS WILD-TYPE 65 30
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                60                 95 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                21                 30 
$`11P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
        2.04        38.24        36.69        18.54        59.24        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY 
        6.28         9.70        59.47        23.08       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48N 
       20.05        14.99        28.80        64.18        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU 
       27.22        14.96         2.07         3.06        66.31        23.54 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       35.67        26.33         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IF-A3RQ 
       12.62        23.97         0.10        41.33         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN 
       25.22        31.76         5.92        22.62         1.05        71.70 
TCGA-K1-A42W TCGA-LI-A9QH TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO 
       27.29         3.88         0.10        37.55         6.35        81.01 
TCGA-QQ-A8VB TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
      175.04         3.88         5.06        72.72        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
       22.62        18.08        27.16         8.81        24.62        12.36 

$`11P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        46.68        31.56        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 
       76.41        66.87        27.81        60.30         8.58        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
        9.04        70.49        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       10.68        44.45        39.35        34.88         9.73        19.30 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        12.49        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A7EF 
       23.44        28.96        17.79        21.63        16.18        21.30 
TCGA-DX-A8BL TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO 
       33.07        19.43         1.15         0.46         0.10        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.07         0.07         9.80        80.48        21.37         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
        3.22         1.38        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-KF-A41W TCGA-LI-A67I 
       73.28         6.28         3.91        36.39        11.70         5.26 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N 
        4.08        75.52        38.63        18.08         5.03         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT 
       93.40        55.50        10.52         0.72         6.58        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7WA 
        0.72        11.93         4.80        41.49        50.89        17.26 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
        8.52        15.65         8.35        32.75        10.82 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.07               0.07 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            175.04             143.41 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             23.31              17.26 
[1] "0.1 - 175.0 (23.3)" "0.1 - 143.4 (17.3)"
[1] "hr=" "1"  
D61V2, continuous
D61V3, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   37 23
  11P LOSS WILD-TYPE 51 45
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     37   23
  11P LOSS WILD-TYPE   51   45
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               37                 51
  MALE                 23                 45
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       2                         2    43
  11P LOSS WILD-TYPE     3                         8    72
D61V4, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   43                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(62) Variable = 11Q LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                 0  1
  11Q LOSS MUTATED   35 16
  11Q LOSS WILD-TYPE 69 35
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                51                104 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                16                 35 
$`11Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R 
        2.04        38.24        36.69        18.54        59.24        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U9 
        6.28         9.70        59.47        23.08        20.05        14.99 
TCGA-DX-A3UD TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BA TCGA-DX-A6BF 
       28.80        12.26        26.47        72.72        66.05         2.07 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO TCGA-FX-A2QS 
       16.18        66.31        23.54        35.67        26.33         0.46 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
       26.89         4.57        12.62         0.10        41.33        80.48 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF 
        7.13        37.12        31.76         5.92        22.62         1.05 
TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-SG-A6Z7 
       27.29         5.26         3.88         7.76       175.04         3.88 
TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WC 
        5.06        72.72        38.27        65.46        22.62        27.16 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X9-A971 
        8.35         8.81        12.36 

$`11Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       14.04        12.85        46.68        31.56        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 
       76.41        66.87        27.81        60.30         8.58        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE 
       42.77         4.54        10.68        44.45        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       25.08        12.49        11.47        23.44        28.96        17.79 
TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BX TCGA-DX-AATS 
       21.63         3.06        21.30        33.07        19.43         1.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z 
        0.10         0.07        20.32         0.07         0.07         4.14 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       23.97         9.80        21.37         8.94         3.22         1.38 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        28.21       143.41       116.88        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-KF-A41W TCGA-MB-A5Y9 
        6.28         3.91        71.70        36.39        11.70         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08        75.52        37.55         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       18.08         5.03         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       18.18        21.01        93.40        55.50        10.52         0.72 
TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        6.58        13.22         0.72        11.93         4.80        41.49 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 
       50.89        17.26        18.08         8.52        15.65        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 
       24.62        10.82 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.10               0.07 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            175.04             143.41 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            22.620             17.935 
[1] "0.1 - 175.0 (22.6)" "0.1 - 143.4 (17.9)"
[1] "hr=" "1.1"
D62V2, continuous
D62V3, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   31 20
  11Q LOSS WILD-TYPE 57 48
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     31   20
  11Q LOSS WILD-TYPE   57   48
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               31                 57
  MALE                 20                 48
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       2                         3    35
  11Q LOSS WILD-TYPE     3                         7    80
D62V4, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                3                  7
  WHITE                                   35                 80
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(63) Variable = 12P LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                 0  1
  12P LOSS MUTATED   26 11
  12P LOSS WILD-TYPE 78 40
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                37                118 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                11                 40 
$`12P LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LY 
        2.04        46.68        74.66         8.58         9.70        17.10 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B7 
       14.99        28.80        64.18        26.47        25.08        12.49 
TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
        2.07         3.06        23.54        21.30        33.07        35.67 
TCGA-DX-A8BO TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ 
       26.33         0.10        23.97        21.37         3.22         7.13 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A9QH TCGA-MJ-A68H TCGA-PC-A5DM 
        6.28         1.05        11.70         3.88         4.47         6.35 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X2-A95T 
        5.03        48.59         3.88        72.72        38.27        50.89 
TCGA-X6-A7WD 
        8.52 

$`12P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04        38.24        12.85        36.69        18.54        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       27.81        60.30        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       70.49       108.13        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        66.05        23.44        28.96        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3RE 
       16.18        66.31        19.43         1.15         0.46         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       20.32         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       12.62         0.10        41.33         9.80        80.48         8.94 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
       71.70        36.39        27.29         5.26         2.37         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        5.69        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        18.08         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       46.82        18.08        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT 
       55.50        10.52         0.72         6.58         5.06        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
        0.72        11.93         4.80        41.49        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08        27.16        15.65         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.10               0.07 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             74.66             175.04 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             14.99              18.92 
[1] "0.1 - 74.7 (15.0)"  "0.1 - 175.0 (18.9)"
[1] "hr=" "1.2"
D63V2, continuous
D63V3, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   21 16
  12P LOSS WILD-TYPE 67 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     21   16
  12P LOSS WILD-TYPE   67   52
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               21                 67
  MALE                 16                 52
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         3    27
  12P LOSS WILD-TYPE     5                         7    88
D63V4, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                3                  7
  WHITE                                   27                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(64) Variable = 12Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                 0  1
  12Q LOSS MUTATED   21 11
  12Q LOSS WILD-TYPE 83 40
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                32                123 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                11                 40 
$`12Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS 
        2.04        46.68        74.66         8.58         9.70         9.04 
TCGA-DX-A3LY TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YU 
       17.10        64.18        26.47        66.05         2.07        23.54 
TCGA-DX-A7EF TCGA-FX-A3NJ TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ 
       21.30         0.10        23.97        21.37         3.22         7.13 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-KF-A41W TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DO 
        6.28         1.05        11.70         4.47         6.35        81.01 
TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-SG-A6Z7 TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X2-A95T 
        5.03        48.59         3.88        72.72        38.27        50.89 
TCGA-X6-A7WD TCGA-X9-A971 
        8.52        12.36 

$`12Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 
       14.04        38.24        12.85        36.69        18.54        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       31.56        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
       27.81        60.30        59.47        54.77        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
      108.13        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        12.49        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A8BL 
       17.79        21.63        16.18         3.06        66.31        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3RE 
       35.67        26.33        19.43         1.15         0.46         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       20.32         0.07         0.07        26.89         4.57         4.14 
TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       12.62         0.10        41.33         9.80        80.48         8.94 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       71.70        36.39        27.29         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        0.49         5.69        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
       75.52        37.55        38.63        18.08         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       46.82        18.08        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT 
       55.50        10.52         0.72         6.58         5.06        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
        0.72        11.93         4.80        41.49        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08        27.16        15.65         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.10               0.07 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             81.01             175.04 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             12.03              19.30 
[1] "0.1 - 81.0 (12.0)"  "0.1 - 175.0 (19.3)"
[1] "hr=" "1.2"
D64V2, continuous
D64V3, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED   22 10
  12Q LOSS WILD-TYPE 66 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     22   10
  12Q LOSS WILD-TYPE   66   58
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE               22                 66
  MALE                 10                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         3    23
  12Q LOSS WILD-TYPE     5                         7    92
D64V4, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                3                  7
  WHITE                                   23                 92
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(65) Variable = 13Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  13Q LOSS MUTATED   52 30
  13Q LOSS WILD-TYPE 52 21
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                82                 73 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                30                 21 
$`13Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R 
       14.04        38.24        36.69        18.54        46.68        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 
        6.28         9.70         9.04        23.08        17.10        20.05 
TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       14.99        39.35        28.80        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB 
       24.26        27.22        14.96        25.08        66.05        23.44 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF 
        2.07        16.18         3.06        66.31        23.54        21.30 
TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-AATS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       33.07        26.33         1.15         0.07        20.32         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       26.89         4.57         4.14        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M4 
        9.80         3.22         7.13        37.12       143.41        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-KF-A41W 
       22.62         1.05         3.91        71.70        27.29        11.70 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
        2.37         5.69         0.10         4.08        37.55         6.35 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       81.01         5.03        46.82        18.08        48.59        18.18 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO 
      175.04        10.52         3.88         6.58         5.06        11.93 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WC 
       72.72        38.27        65.46        22.62        17.26        27.16 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
        8.35         8.81        32.75        24.62 

$`13Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
        2.04        12.85        59.24        31.56        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       76.41        66.87        27.81        60.30         8.58        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       54.77        70.49       108.13        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48N TCGA-DX-A48R 
        4.54        10.68        44.45        34.88        12.26        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       72.72        12.49        11.47        28.96        17.79        21.63 
TCGA-DX-A8BM TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HS-A5N9 
       35.67        19.43         0.46         0.10         0.07        41.33 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         8.94         1.38        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A3PO 
       28.21       116.88        13.58         5.92         6.28        36.39 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        5.26         3.88         0.49         4.47        11.08        15.65 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VD 
       75.52        38.63        18.08         7.76         1.84        21.01 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ 
       93.40        55.50         0.72        13.22         0.72         4.80 
TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C7 
       41.49        50.89        18.08         8.52        15.65        10.82 
TCGA-X9-A971 
       12.36 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              0.07               0.07 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            175.04             116.88 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             18.92              18.08 
[1] "0.1 - 175.0 (18.9)" "0.1 - 116.9 (18.1)"
[1] "hr=" "1.4"
D65V2, continuous
D65V3, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED   53 29
  13Q LOSS WILD-TYPE 35 39
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED     53   29
  13Q LOSS WILD-TYPE   35   39
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE               53                 35
  MALE                 29                 39
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       3                         5    63
  13Q LOSS WILD-TYPE     2                         5    52
D65V4, multiclass
                           clus
vv                          13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  ASIAN                                    3                  2
  BLACK OR AFRICAN AMERICAN                5                  5
  WHITE                                   63                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(66) Variable = 14Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   30  7
  14Q LOSS WILD-TYPE 74 44
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                37                118 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 7                 44 
$`14Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R 
       14.04         2.04        38.24        36.69        59.24        74.66 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A48N TCGA-DX-A48O 
       23.08        70.49        17.10        15.06        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6YU TCGA-DX-A8BM TCGA-DX-A8BO 
       14.96        72.72        12.49        23.54        35.67        26.33 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-HS-A5N8 TCGA-HS-A5NA 
        0.46         0.10         0.07         0.07         0.10         9.80 
TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
        3.22        37.12        28.21       143.41       116.88        73.28 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-SI-AA8B TCGA-X6-A7WB 
        6.28         1.05         5.03        46.82         5.06        18.08 
TCGA-X6-A8C2 
       15.65 

$`14Q LOSS WILD-TYPE`
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       12.85        18.54        46.68        31.56        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 
        9.70        59.47        54.77         9.04       108.13        20.05 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       24.26        26.47        25.08        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A3RE 
       66.31        21.30        33.07        19.43         1.15         0.07 
TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       20.32        26.89         4.57         4.14        12.62        23.97 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ 
       41.33        80.48        21.37         8.94         1.38         7.13 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A75J 
       25.22        31.76        13.58         5.92        22.62         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       71.70        36.39        27.29        11.70         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01        18.08         7.76         1.84        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.18        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        0.72         3.88         6.58        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       50.89        17.26        27.16         8.52         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.07               0.07 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            143.41             175.04 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             17.10              18.92 
[1] "0.1 - 143.4 (17.1)" "0.1 - 175.0 (18.9)"
[1] "hr=" "2"  
D66V2, continuous
D66V3, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   21 16
  14Q LOSS WILD-TYPE 67 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     21   16
  14Q LOSS WILD-TYPE   67   52
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               21                 67
  MALE                 16                 52
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         2    28
  14Q LOSS WILD-TYPE     5                         8    87
D66V4, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   28                 87
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(67) Variable = 15Q LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   14 14
  15Q LOSS WILD-TYPE 90 37
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                28                127 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                14                 37 
$`15Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3UA TCGA-DX-A3UB 
       14.04         2.04         9.04        23.08        10.68        44.45 
TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM 
       26.47         2.07         3.06        21.30        33.07        35.67 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       20.32         0.07         4.57        37.12       143.41         5.92 
TCGA-JV-A5VE TCGA-KF-A41W TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A8VH 
        6.28        11.70         6.35         5.03         7.76        10.52 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7WB TCGA-X6-A8C6 
       38.27        22.62        18.08        24.62 

$`15Q LOSS WILD-TYPE`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.24        12.85        36.69        18.54        46.68        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       31.56        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       54.77        70.49       108.13        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75        42.77         4.54        14.99        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       27.22        14.96        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        23.44        28.96        17.79        21.63        16.18 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
       66.31        23.54        26.33        19.43         1.15         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 
        0.10         0.07         0.07        26.89         4.14        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
        8.94         3.22         1.38         7.13        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VF 
       28.21       116.88        13.58        73.28        22.62         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH 
        3.91        71.70        36.39        27.29         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        0.10         4.08        75.52        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
       18.08         1.84        46.82        18.08        48.59        18.18 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 
       21.01       175.04        93.40        55.50         0.72         3.88 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        6.58         5.06        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC 
       72.72        41.49        65.46        50.89        17.26        27.16 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
        8.52        15.65         8.35         8.81        32.75        10.82 
TCGA-X9-A971 
       12.36 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.07               0.07 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
            143.41             175.04 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             12.87              19.30 
[1] "0.1 - 143.4 (12.9)" "0.1 - 175.0 (19.3)"
[1] "hr=" "2.4"
D67V2, continuous
D67V3, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   15 14
  15Q LOSS WILD-TYPE 73 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     15   14
  15Q LOSS WILD-TYPE   73   54
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               15                 73
  MALE                 14                 54
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         2    25
  15Q LOSS WILD-TYPE     5                         8    90
D67V4, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(68) Variable = 16P LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                 0  1
  16P LOSS MUTATED   34 13
  16P LOSS WILD-TYPE 70 38
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                47                108 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                13                 38 
$`16P LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U7 
       18.54        59.24        74.66         6.28        23.08        42.77 
TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48O TCGA-DX-A6BA TCGA-DX-A8BO 
       10.68        28.80        64.18        27.22        66.05        26.33 
TCGA-DX-AATS TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        1.15        20.32         0.07         4.57         4.14        12.62 
TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE 
        0.10         3.22         7.13        37.12       143.41         6.28 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-KF-A41W TCGA-MB-A8JL TCGA-MJ-A68H TCGA-N1-A6IA 
        1.05        71.70        11.70         5.69         4.47         4.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH 
        5.03         7.76        46.82        18.18        21.01        10.52 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 
        6.58         5.06         0.72        72.72        38.27        22.62 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 
       18.08         8.52        15.65         8.81        24.62 

$`16P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        36.69        46.68 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       31.56        42.54         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        14.99        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        12.26        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.08        12.49        11.47        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        66.31        23.54 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ 
       21.30        33.07        35.67        19.43         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
        0.07         0.07        26.89        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         8.94         1.38        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       28.21       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
        3.91        36.39        27.29         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
        0.49        11.08        15.65         0.10        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
        6.35        38.63        81.01        18.08         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 
       48.59       175.04        93.40        55.50         0.72         3.88 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T 
       13.22        11.93         4.80        41.49        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       17.26        27.16         8.35        32.75        10.82        12.36 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.07               0.07 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            143.41             175.04 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
            12.620             20.675 
[1] "0.1 - 143.4 (12.6)" "0.1 - 175.0 (20.7)"
[1] "hr=" "1"  
D68V2, continuous
D68V3, binary
                    cls
clus                  0  1
  16P LOSS MUTATED   31 16
  16P LOSS WILD-TYPE 57 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED     31   16
  16P LOSS WILD-TYPE   57   52
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE               31                 57
  MALE                 16                 52
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       1                         5    36
  16P LOSS WILD-TYPE     4                         5    79
D68V4, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                5                  5
  WHITE                                   36                 79
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(69) Variable = 16Q LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  16Q LOSS MUTATED   55 23
  16Q LOSS WILD-TYPE 49 28
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                78                 77 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                23                 28 
$`16Q LOSS MUTATED`
TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 
       14.04        18.54        59.24        74.66         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC 
       23.08        17.10        42.77        14.99        10.68        39.35 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       28.80        64.18        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A8BO TCGA-DX-AATS 
       26.47        25.08        66.05        23.44        26.33         1.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA 
        4.57         4.14        12.62        23.97         0.10         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF 
       25.22        31.76        13.58        73.28         6.28         1.05 
TCGA-K1-A3PN TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R 
       71.70        11.70         3.88         5.69         4.47         0.10 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N 
        4.08        37.55        81.01        18.08         5.03         7.76 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VH TCGA-SG-A849 
       46.82        48.59        18.18        21.01        10.52         6.58 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X6-A7WA 
        5.06         0.72        72.72        38.27        65.46        17.26 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08         8.52        15.65         8.81        32.75        24.62 

$`16Q LOSS WILD-TYPE`
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        2.04        38.24        12.85        36.69        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE 
       20.05        15.06        17.75         4.54        44.45        34.88 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE 
        9.73        12.26        72.72        12.49        11.47        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
        2.07        17.79        21.63        16.18         3.06        66.31 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-FX-A2QS 
       23.54        21.30        33.07        35.67        19.43         0.46 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 
       41.33        80.48        28.21       143.41       116.88         5.92 
TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-MB-A5Y9 
       22.62         3.91        36.39        27.29         5.26         2.37 
TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MJ-A850 TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN 
        0.49        11.08        15.65        75.52         6.35        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        1.84        18.08       175.04        93.40        55.50         0.72 
TCGA-SG-A6Z7 TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8Y0 
        3.88        13.22        11.93         4.80        41.49        22.62 
TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 
       50.89        27.16         8.35        10.82        12.36 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.07               0.46 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             81.01             175.04 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             17.18              21.63 
[1] "0.1 - 81.0 (17.2)"  "0.5 - 175.0 (21.6)"
[1] "hr=" "1.1"
D69V2, continuous
D69V3, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED   50 28
  16Q LOSS WILD-TYPE 38 40
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     50   28
  16Q LOSS WILD-TYPE   38   40
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE               50                 38
  MALE                 28                 40
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       2                         7    61
  16Q LOSS WILD-TYPE     3                         3    54
D69V4, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    2                  3
  BLACK OR AFRICAN AMERICAN                7                  3
  WHITE                                   61                 54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(70) Variable = 17P LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   17 13
  17P LOSS WILD-TYPE 87 38
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                30                125 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                13                 38 
$`17P LOSS MUTATED`
TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A6BB 
       36.69        74.66        23.08        14.99        10.68        23.44 
TCGA-DX-A7EF TCGA-DX-AATS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HS-A5N8 
       21.30         1.15         0.10         0.07        26.89         0.10 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 
       41.33        80.48         3.22         1.38        25.22        28.21 
TCGA-IS-A3K7 TCGA-K1-A42W TCGA-KF-A41W TCGA-MB-A5YA TCGA-PC-A5DL TCGA-QQ-A5VC 
      143.41        27.29        11.70         0.49        37.55        18.18 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WK-A8XY 
       10.52         3.88         5.06        11.93        38.27        65.46 

$`17P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        18.54        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        31.56        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       12.49        11.47        66.05        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL 
       21.63        16.18         3.06        66.31        23.54        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO 
       35.67        26.33        19.43         0.46         0.07        20.32 
TCGA-FX-A48G TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
        0.07         4.57         4.14        12.62        23.97         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K8 
       21.37         8.94         7.13        37.12        31.76       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62         6.28         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
        3.91        71.70        36.39         5.26         3.88         2.37 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA 
        5.69         4.47        11.08        15.65         0.10         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
       75.52         6.35        38.63        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
        7.76         1.84        46.82        18.08        48.59        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT 
      175.04        93.40        55.50         0.72         6.58        13.22 
TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-X2-A95T 
        0.72         4.80        72.72        41.49        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       17.26        18.08        27.16         8.52        15.65         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        32.75        24.62        10.82        12.36 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.07               0.07 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            143.41             175.04 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
             19.74              18.08 
[1] "0.1 - 143.4 (19.7)" "0.1 - 175.0 (18.1)"
[1] "hr=" "1.5"
D70V2, continuous
D70V3, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   18 12
  17P LOSS WILD-TYPE 70 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     18   12
  17P LOSS WILD-TYPE   70   56
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               18                 70
  MALE                 12                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       0                         1    25
  17P LOSS WILD-TYPE     5                         9    90
D70V4, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(71) Variable = 17Q LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                 0  1
  17Q LOSS MUTATED   14 12
  17Q LOSS WILD-TYPE 90 39
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                26                129 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                12                 39 
$`17Q LOSS MUTATED`
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE 
       74.66         6.28        23.08        14.99        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A7EF TCGA-DX-AATS TCGA-FX-A3NJ 
       64.18        24.26        66.05        21.30         1.15         0.10 
TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ 
       26.89         0.10        41.33        80.48         3.22        25.22 
TCGA-K1-A42W TCGA-KF-A41W TCGA-PC-A5DL TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-WK-A8XX 
       27.29        11.70        37.55        10.52         3.88        38.27 
TCGA-X6-A7WC TCGA-X6-A8C6 
       27.16        24.62 

$`17Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       46.68        59.24        31.56        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       39.35         9.73        19.30        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       26.47        72.72        25.08        12.49        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         2.07        17.79        21.63        16.18         3.06 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX 
       66.31        23.54        33.07        35.67        26.33        19.43 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3YV 
        0.46         0.07        20.32         0.07         0.07         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
        4.14        12.62        23.97         9.80        21.37         8.94 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38         7.13        37.12        31.76        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62         6.28 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-LI-A67I TCGA-LI-A9QH 
        1.05         3.91        71.70        36.39         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        0.10         4.08        75.52         6.35        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08         5.03         7.76         1.84        46.82        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG 
       48.59        18.18        21.01       175.04        93.40        55.50 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO 
        0.72         6.58         5.06        13.22         0.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
        4.80        72.72        41.49        65.46        22.62        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       17.26        18.08         8.52        15.65         8.35         8.81 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        10.82        12.36 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.10               0.07 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             80.48             175.04 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             24.92              17.79 
[1] "0.1 - 80.5 (24.9)"  "0.1 - 175.0 (17.8)"
[1] "hr=" "1.5"
D71V2, continuous
D71V3, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   14 12
  17Q LOSS WILD-TYPE 74 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     14   12
  17Q LOSS WILD-TYPE   74   56
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               14                 74
  MALE                 12                 56
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       0                         1    21
  17Q LOSS WILD-TYPE     5                         9    94
D71V4, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   21                 94
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(72) Variable = 18P LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                 0  1
  18P LOSS MUTATED   19 14
  18P LOSS WILD-TYPE 85 37
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                33                122 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                14                 37 
$`18P LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U9 
       38.24        12.85        18.54         9.70        23.08        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48P TCGA-DX-A6BF TCGA-HB-A2OT 
       10.68        39.35        64.18        14.96         2.07        26.89 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M4 
       23.97        80.48        21.37         3.22       143.41        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-KF-A41W TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QC-A7B5 
       22.62         1.05        11.70        37.55        18.08         5.03 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 
       10.52         3.88         5.06        72.72        38.27        22.62 
TCGA-X6-A7WB TCGA-X6-A8C4 TCGA-X6-A8C6 
       18.08         8.81        24.62 

$`18P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        36.69        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       42.54        74.66         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       70.49       108.13        17.10        20.05        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       42.77         4.54        44.45        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        12.49        11.47        66.05        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        66.31        23.54 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS 
       21.30        33.07        35.67        26.33        19.43         1.15 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57         4.14        12.62         0.10        41.33         9.80 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        8.94         1.38         7.13        37.12        25.22        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J 
       28.21       116.88        13.58         5.92         6.28         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       71.70        36.39        27.29         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
        4.08        75.52         6.35        38.63        81.01         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT 
      175.04        93.40        55.50         0.72         6.58        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T 
        0.72        11.93         4.80        41.49        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       17.26        27.16         8.52        15.65         8.35        32.75 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              1.05               0.07 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            143.41             175.04 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
             18.54              18.13 
[1] "1.1 - 143.4 (18.5)" "0.1 - 175.0 (18.1)"
[1] "hr=" "1.4"
D72V2, continuous
D72V3, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   23 10
  18P LOSS WILD-TYPE 65 58
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     23   10
  18P LOSS WILD-TYPE   65   58
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               23                 65
  MALE                 10                 58
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       1                         2    25
  18P LOSS WILD-TYPE     4                         8    90
D72V4, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   25                 90
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(73) Variable = 18Q LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                 0  1
  18Q LOSS MUTATED   22 15
  18Q LOSS WILD-TYPE 82 36
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                37                118 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                15                 36 
$`18Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT 
       38.24        12.85        18.54         6.28         9.70        23.08 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A6BA 
       14.99        10.68        64.18        19.30        14.96        66.05 
TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A8BO TCGA-FX-A48G TCGA-HB-A2OT 
        2.07         3.06        66.31        26.33         0.07        26.89 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M6 
       23.97        80.48         3.22        25.22       143.41        22.62 
TCGA-JV-A5VF TCGA-KF-A41W TCGA-LI-A67I TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A7B5 
        1.05        11.70         5.26         6.35        18.08         5.03 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8Y0 
      175.04        10.52         3.88         5.06        72.72        22.62 
TCGA-X6-A8C6 
       24.62 

$`18Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       14.04         2.04        36.69        46.68        59.24        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       42.54        74.66         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       60.30         8.58        59.47        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       12.49        11.47        23.44        28.96        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX 
       16.18        23.54        21.30        33.07        35.67        19.43 
TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y 
        1.15         0.46         0.10         0.07        20.32         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57         4.14        12.62         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK 
       21.37         8.94         1.38         7.13        37.12        31.76 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       28.21       116.88        13.58        73.28         5.92         6.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A9QH TCGA-MB-A5Y9 
        3.91        71.70        36.39        27.29         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
        4.08        75.52        37.55        38.63        81.01         7.76 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       93.40        55.50         0.72         6.58        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
       11.93         4.80        41.49        38.27        65.46        50.89 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       17.26        18.08        27.16         8.52        15.65         8.35 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
        8.81        32.75        10.82        12.36 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.07               0.07 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            175.04             116.88 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            18.080             18.805 
[1] "0.1 - 175.0 (18.1)" "0.1 - 116.9 (18.8)"
[1] "hr=" "1.4"
D73V2, continuous
D73V3, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   24 13
  18Q LOSS WILD-TYPE 64 55
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     24   13
  18Q LOSS WILD-TYPE   64   55
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               24                 64
  MALE                 13                 55
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       1                         2    27
  18Q LOSS WILD-TYPE     4                         8    88
D73V4, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   27                 88
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(74) Variable = 19P LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                 0  1
  19P LOSS MUTATED    9  4
  19P LOSS WILD-TYPE 95 47
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                13                142 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 47 
$`19P LOSS MUTATED`
TCGA-DX-A3LT TCGA-IE-A4EH TCGA-IW-A3M6 TCGA-KF-A41W TCGA-LI-A67I TCGA-PC-A5DM 
       23.08        21.37        22.62        11.70         5.26         6.35 
TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8Y0 TCGA-X6-A8C2 
       81.01         5.03         3.88         5.06        22.62        15.65 
TCGA-X6-A8C4 
        8.81 

$`19P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        20.05        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        12.49        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         2.07        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL 
       16.18         3.06        66.31        23.54        21.30        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ 
       35.67        26.33        19.43         1.15         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.07        20.32         0.07         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       73.28         5.92         6.28         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        27.29         3.88         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        4.47        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55        38.63        18.08         7.76         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       18.08        48.59        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       55.50        10.52         0.72         6.58        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 
       50.89        17.26        18.08        27.16         8.52         8.35 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       32.75        24.62        10.82        12.36 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              3.88               0.07 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             81.01             175.04 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             11.70              18.92 
[1] "3.9 - 81.0 (11.7)"  "0.1 - 175.0 (18.9)"
[1] "hr=" "1.3"
D74V2, continuous
D74V3, binary
                    cls
clus                  0  1
  19P LOSS MUTATED    9  4
  19P LOSS WILD-TYPE 79 64
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      9    4
  19P LOSS WILD-TYPE   79   64
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE                9                 79
  MALE                  4                 64
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       1                         0    12
  19P LOSS WILD-TYPE     4                        10   103
D74V4, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   12                103
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(75) Variable = 19Q LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                 0  1
  19Q LOSS MUTATED   14  7
  19Q LOSS WILD-TYPE 90 44
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                134 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 7                 44 
$`19Q LOSS MUTATED`
TCGA-DX-A1L0 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3UD TCGA-DX-A8BO 
       18.54         9.70        23.08        42.77        28.80        26.33 
TCGA-FX-A48G TCGA-IE-A4EH TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-LI-A67I 
        0.07        21.37        73.28        22.62         3.91         5.26 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-SG-A6Z7 TCGA-SI-AA8B 
       75.52         6.35        81.01         5.03         3.88         5.06 
TCGA-WK-A8Y0 TCGA-X6-A8C2 TCGA-X6-A8C4 
       22.62        15.65         8.81 

$`19Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       14.04         2.04        38.24        12.85        36.69        46.68 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        31.56        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 
       66.87         6.28        27.81        60.30         8.58        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       39.35        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       12.49        11.47        66.05        23.44        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU 
       17.79        21.63        16.18         3.06        66.31        23.54 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
       21.30        33.07        35.67        19.43         1.15         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.10         0.07        20.32         0.07        26.89         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.14        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48         8.94         3.22         1.38         7.13        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        31.76        28.21       143.41       116.88        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92         6.28         1.05        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       11.70         3.88         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN 
       11.08        15.65         0.10         4.08        37.55        38.63 
TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       18.08         7.76         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       18.18        21.01       175.04        93.40        55.50        10.52 
TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
        0.72         6.58        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
       72.72        41.49        38.27        65.46        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08        27.16         8.52         8.35        32.75        24.62 
TCGA-X6-A8C7 TCGA-X9-A971 
       10.82        12.36 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.07               0.07 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             81.01             175.04 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             18.54              18.13 
[1] "0.1 - 81.0 (18.5)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.1"
D75V2, continuous
D75V3, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   12  9
  19Q LOSS WILD-TYPE 76 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     12    9
  19Q LOSS WILD-TYPE   76   59
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               12                 76
  MALE                  9                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       1                         0    18
  19Q LOSS WILD-TYPE     4                        10    97
D75V4, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                0                 10
  WHITE                                   18                 97
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(76) Variable = 20P LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  20P LOSS MUTATED   18  8
  20P LOSS WILD-TYPE 86 43
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                26                129 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 8                 43 
$`20P LOSS MUTATED`
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE 
        9.04        23.08        17.10        20.05        14.99        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48V TCGA-DX-A8BO TCGA-FX-A2QS 
       64.18        19.30        24.26        25.08        26.33         0.46 
TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-K1-A3PN TCGA-PC-A5DK TCGA-PC-A5DO TCGA-QQ-A5VC 
        7.13         6.28        71.70        75.52        81.01        18.18 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-X6-A7WB 
        6.58         5.06        11.93        72.72        65.46        18.08 
TCGA-X6-A8C4 TCGA-X9-A971 
        8.81        12.36 

$`20P LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
        9.70        59.47        54.77        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       28.80         9.73        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        12.49        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
        2.07        17.79        21.63        16.18         3.06        66.31 
TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-AATS 
       23.54        21.30        33.07        35.67        19.43         1.15 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         1.05         3.91 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
       36.39        27.29        11.70         5.26         3.88         2.37 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R 
        0.49         5.69         4.47        11.08        15.65         0.10 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 
        4.08        37.55         6.35        38.63        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
        7.76         1.84        46.82        18.08        48.59        21.01 
TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 
      175.04        93.40        55.50        10.52         0.72         3.88 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8Y0 
       13.22         0.72         4.80        41.49        38.27        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       50.89        17.26        27.16         8.52        15.65         8.35 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       32.75        24.62        10.82 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.46               0.07 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             81.01             175.04 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             18.74              18.08 
[1] "0.5 - 81.0 (18.7)"  "0.1 - 175.0 (18.1)"
[1] "hr=" "1.2"
D76V2, continuous
D76V3, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   18  9
  20P LOSS WILD-TYPE 70 59
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     18    9
  20P LOSS WILD-TYPE   70   59
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               18                 70
  MALE                  9                 59
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         1    26
  20P LOSS WILD-TYPE     5                         9    89
D76V4, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   26                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(77) Variable = 20Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  20Q LOSS MUTATED    7  4
  20Q LOSS WILD-TYPE 97 47
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                11                144 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
                 4                 47 
$`20Q LOSS MUTATED`
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UE 
        9.04        23.08        17.10        20.05        14.99        34.88 
TCGA-IE-A6BZ TCGA-JV-A5VE TCGA-WK-A8XO TCGA-WK-A8XS TCGA-X9-A971 
        7.13         6.28        11.93        72.72        12.36 

$`20Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
       14.04         2.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       46.68        59.24        31.56        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
        9.70        59.47        54.77        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        12.49 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         2.07        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF 
       21.63        16.18         3.06        66.31        23.54        21.30 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
       33.07        35.67        26.33        19.43         1.15         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT 
        0.10         0.07        20.32         0.07         0.07        26.89 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        31.76        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28         5.92        22.62         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
       71.70        36.39        27.29        11.70         5.26         3.88 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        2.37         0.49         5.69         4.47        11.08        15.65 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
        0.10         4.08        75.52        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       81.01        18.08         5.03         7.76         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF 
       18.08        48.59        18.18        21.01       175.04        93.40 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B 
       55.50        10.52         0.72         3.88         6.58         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       13.22         0.72         4.80        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
       22.62        50.89        17.26        18.08        27.16         8.52 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       15.65         8.35         8.81        32.75        24.62        10.82 

  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
              6.28               0.07 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             72.72             175.04 
  20Q LOSS MUTATED 20Q LOSS WILD-TYPE 
             14.99              18.92 
[1] "6.3 - 72.7 (15.0)"  "0.1 - 175.0 (18.9)"
[1] "hr=" "1.4"
D77V2, continuous
D77V3, binary
                    cls
clus                  0  1
  20Q LOSS MUTATED    7  5
  20Q LOSS WILD-TYPE 81 63
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q LOSS MUTATED      7    5
  20Q LOSS WILD-TYPE   81   63
        clus
vv       20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  FEMALE                7                 81
  MALE                  5                 63
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q LOSS MUTATED       0                         1    11
  20Q LOSS WILD-TYPE     5                         9   104
D77V4, multiclass
                           clus
vv                          20Q LOSS MUTATED 20Q LOSS WILD-TYPE
  ASIAN                                    0                  5
  BLACK OR AFRICAN AMERICAN                1                  9
  WHITE                                   11                104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(78) Variable = 21Q LOSS MUTATION ANALYSIS
D78V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   28  6
  21Q LOSS WILD-TYPE 76 45
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                34                121 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                 6                 45 
$`21Q LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY 
       38.24        18.54        59.24        74.66         6.28        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UF TCGA-DX-A48V TCGA-DX-A6BB TCGA-DX-A6BF 
       20.05        15.06        64.18        25.08        23.44         2.07 
TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-AATS TCGA-FX-A3TO TCGA-HB-A2OT 
       21.30        35.67        26.33         1.15        20.32        26.89 
TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-KF-A41W 
      143.41        22.62         6.28        71.70        27.29        11.70 
TCGA-PC-A5DO TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B 
       81.01       175.04        55.50         3.88         6.58         5.06 
TCGA-WK-A8XS TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 
       72.72        15.65         8.81        24.62 

$`21Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
       14.04         2.04        12.85        36.69        46.68        31.56 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       70.49       108.13        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG 
       72.72        12.49        11.47        66.05        28.96        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL 
       21.63        16.18         3.06        66.31        23.54        33.07 
TCGA-DX-A8BX TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       19.43         0.46         0.10         0.07         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        4.57         4.14        12.62        23.97         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
        9.80        80.48        21.37         8.94         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        7.13        37.12        25.22        31.76        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
       13.58        73.28         5.92         1.05         3.91        36.39 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
        5.26         3.88         2.37         0.49         5.69         4.47 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       11.08        15.65         0.10         4.08        75.52        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        38.63        18.08         5.03         7.76         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF 
       46.82        18.08        48.59        18.18        21.01        93.40 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
       10.52         0.72        13.22         0.72        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46        22.62        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.08        27.16         8.52         8.35        32.75        10.82 
TCGA-X9-A971 
       12.36 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              1.15               0.07 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            175.04             116.88 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             23.03              17.75 
[1] "1.1 - 175.0 (23.0)" "0.1 - 116.9 (17.8)"
[1] "hr=" "2.8"
D78V2, continuous
D78V3, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   19 15
  21Q LOSS WILD-TYPE 69 53
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     19   15
  21Q LOSS WILD-TYPE   69   53
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               19                 69
  MALE                 15                 53
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       1                         2    26
  21Q LOSS WILD-TYPE     4                         8    89
D78V4, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   26                 89
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(79) Variable = 22Q LOSS MUTATION ANALYSIS
D79V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   30 15
  22Q LOSS WILD-TYPE 74 36
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                45                110 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                15                 36 
$`22Q LOSS MUTATED`
TCGA-DX-A1KW TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A2IZ 
        2.04        46.68        59.24        66.87         6.28         8.58 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A48L 
        9.04        23.08       108.13        20.05        14.99        24.26 
TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A8BL 
       26.47        66.05        16.18        66.31        23.54        33.07 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5NA 
        0.07        20.32         0.07         4.57         0.10         9.80 
TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 
       21.37         7.13        25.22       143.41       116.88         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-KF-A41W TCGA-LI-A67I TCGA-QC-AA9N 
       22.62         1.05        71.70        11.70         5.26         7.76 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SI-AA8B TCGA-WK-A8XS TCGA-X2-A95T 
      175.04        10.52         3.88         5.06        72.72        50.89 
TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X9-A971 
       18.08        15.65        12.36 

$`22Q LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 
       14.04        38.24        12.85        36.69        18.54        31.56 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 
       42.54        74.66         5.26        76.41        27.81        60.30 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U5 
        9.70        59.47        54.77        70.49        17.10        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       28.80        34.88        64.18         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       27.22        14.96        72.72        25.08        12.49        11.47 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       23.44        28.96         2.07        17.79        21.63         3.06 
TCGA-DX-A7EF TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS 
       21.30        35.67        26.33        19.43         1.15         0.46 
TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.10         0.07        26.89         4.14        12.62        23.97 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ 
       41.33        80.48         8.94         3.22         1.38        37.12 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J 
       31.76        28.21        13.58        73.28         6.28         3.91 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       36.39        27.29         3.88         2.37         0.49         5.69 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        4.47        11.08        15.65         0.10         4.08        75.52 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
       37.55         6.35        38.63        81.01        18.08         5.03 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        18.18        21.01 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT TCGA-UE-A6QU 
       93.40        55.50         0.72         6.58        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        41.49        38.27        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       17.26        27.16         8.52         8.35         8.81        32.75 
TCGA-X6-A8C6 TCGA-X6-A8C7 
       24.62        10.82 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.07               0.07 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
            175.04              93.40 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             18.08              18.36 
[1] "0.1 - 175.0 (18.1)" "0.1 - 93.4 (18.4)" 
[1] "hr=" "1.1"
D79V2, continuous
D79V3, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   29 16
  22Q LOSS WILD-TYPE 59 52
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     29   16
  22Q LOSS WILD-TYPE   59   52
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               29                 59
  MALE                 16                 52
[1] 2 2
[1] FALSE
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       1                         2    34
  22Q LOSS WILD-TYPE     4                         8    81
D79V4, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    1                  4
  BLACK OR AFRICAN AMERICAN                2                  8
  WHITE                                   34                 81
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(80) Variable = XQ LOSS MUTATION ANALYSIS
D80V1, survival
                   sevent
clus2                0  1
  XQ LOSS MUTATED   42 17
  XQ LOSS WILD-TYPE 62 34
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               59                96 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               17                34 
$`XQ LOSS MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-DX-A3LW 
       38.24        12.85        18.54        59.24         9.70       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       17.10        20.05        10.68        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       64.18         9.73        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YU 
       25.08        12.49        11.47        66.05        23.44        23.54 
TCGA-DX-A7EF TCGA-DX-A8BL TCGA-DX-A8BM TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV 
       21.30        33.07        35.67        20.32         0.07         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IF-A3RQ TCGA-IF-A4AJ 
       12.62        23.97         9.80        21.37        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-LI-A9QH 
       28.21       143.41        73.28        22.62         6.28         3.88 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5VC 
        5.69         4.47        38.63        81.01         7.76        18.18 
TCGA-QQ-A8VB TCGA-UE-A6QU TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA 
      175.04         0.72        38.27        65.46        50.89        17.26 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08         8.52        15.65         8.81        32.75 

$`XQ LOSS WILD-TYPE`
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04         2.04        36.69        46.68        31.56        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         8.58        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       70.49        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF 
       44.45        19.30        24.26        12.26        28.96         2.07 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A8BO 
       17.79        21.63        16.18         3.06        66.31        26.33 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y 
       19.43         1.15         0.46         0.10         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI 
       26.89         4.14         0.10        41.33        80.48         8.94 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IS-A3KA 
        3.22         1.38         7.13        31.76       116.88        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
        5.92         1.05         3.91        71.70        36.39        27.29 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MJ-A850 
       11.70         5.26         2.37         0.49        11.08        15.65 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP 
        0.10         4.08        75.52        37.55         6.35        18.08 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
        5.03         1.84        46.82        18.08        48.59        21.01 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 
       93.40        55.50        10.52         0.72         3.88         6.58 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        5.06        13.22        11.93         4.80        72.72        41.49 
TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       22.62        27.16         8.35        24.62        10.82        12.36 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.07              0.07 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           175.04            116.88 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           22.620            15.355 
[1] "0.1 - 175.0 (22.6)" "0.1 - 116.9 (15.4)"
[1] "hr=" "1.5"
D80V2, continuous
D80V3, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   38 21
  XQ LOSS WILD-TYPE 50 47
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     38   21
  XQ LOSS WILD-TYPE   50   47
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              38                50
  MALE                21                47
[1] 2 2
[1] FALSE
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       2                         6    44
  XQ LOSS WILD-TYPE     3                         4    71
D80V4, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   2                 3
  BLACK OR AFRICAN AMERICAN               6                 4
  WHITE                                  44                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
