[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"        "-oTREAD-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/READ-TP/10006188/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/10013796/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=162, common to both=162
[1] "Reduce the number of clustering variables from 80 to 78."
[1]  78 162
[1] "1P GAIN MUTATION ANALYSIS"
[1] 3
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               150 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               12               150 
[1] "1Q GAIN MUTATION ANALYSIS"
[1] 3
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               130 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               32               130 
[1] "2P GAIN MUTATION ANALYSIS"
[1] 3
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39               123 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               39               123 
[1] "2Q GAIN MUTATION ANALYSIS"
[1] 3
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               121 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               41               121 
[1] "3P GAIN MUTATION ANALYSIS"
[1] 3
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               27               135 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               27               135 
[1] "3Q GAIN MUTATION ANALYSIS"
[1] 3
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               34               128 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               34               128 
[1] "4P GAIN MUTATION ANALYSIS"
[1] 3
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               153 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                9               153 
[1] "4Q GAIN MUTATION ANALYSIS"
[1] 3
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               157 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               157 
[1] "5P GAIN MUTATION ANALYSIS"
[1] 3
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               34               128 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               34               128 
[1] "5Q GAIN MUTATION ANALYSIS"
[1] 3
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               22               140 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               22               140 
[1] "6P GAIN MUTATION ANALYSIS"
[1] 3
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               40               122 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               40               122 
[1] "6Q GAIN MUTATION ANALYSIS"
[1] 3
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               35               127 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               35               127 
[1] "7P GAIN MUTATION ANALYSIS"
[1] 3
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              100                62 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
              100                62 
[1] "7Q GAIN MUTATION ANALYSIS"
[1] 3
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               83                79 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               83                79 
[1] "8P GAIN MUTATION ANALYSIS"
[1] 3
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               123 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               39               123 
[1] "8Q GAIN MUTATION ANALYSIS"
[1] 3
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               88                74 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               88                74 
[1] "9P GAIN MUTATION ANALYSIS"
[1] 3
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               42               120 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               42               120 
[1] "9Q GAIN MUTATION ANALYSIS"
[1] 3
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               129 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               33               129 
[1] "10P GAIN MUTATION ANALYSIS"
[1] 3
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                12                150 
[1] "10Q GAIN MUTATION ANALYSIS"
[1] 3
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                156 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 6                156 
[1] "11P GAIN MUTATION ANALYSIS"
[1] 3
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                132 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                30                132 
[1] "11Q GAIN MUTATION ANALYSIS"
[1] 3
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                137 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                25                137 
[1] "12P GAIN MUTATION ANALYSIS"
[1] 3
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                129 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                33                129 
[1] "12Q GAIN MUTATION ANALYSIS"
[1] 3
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                23                139 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                23                139 
[1] "13Q GAIN MUTATION ANALYSIS"
[1] 3
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               110                 52 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               110                 52 
[1] "14Q GAIN MUTATION ANALYSIS"
[1] 3
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                154 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 8                154 
[1] "15Q GAIN MUTATION ANALYSIS"
[1] 3
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                159 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                159 
[1] "16P GAIN MUTATION ANALYSIS"
[1] 3
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                39                123 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                39                123 
[1] "16Q GAIN MUTATION ANALYSIS"
[1] 3
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                39                123 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                39                123 
[1] "17P GAIN MUTATION ANALYSIS"
[1] 3
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                154 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                154 
[1] "17Q GAIN MUTATION ANALYSIS"
[1] 3
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                132 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                30                132 
[1] "18P GAIN MUTATION ANALYSIS"
[1] 3
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                154 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 8                154 
[1] "18Q GAIN MUTATION ANALYSIS"
[1] 3
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                156 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 6                156 
[1] "19P GAIN MUTATION ANALYSIS"
[1] 3
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                131 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                31                131 
[1] "19Q GAIN MUTATION ANALYSIS"
[1] 3
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                30                132 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                30                132 
[1] "20P GAIN MUTATION ANALYSIS"
[1] 3
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               104                 58 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
               104                 58 
[1] "20Q GAIN MUTATION ANALYSIS"
[1] 3
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               142                 20 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               142                 20 
[1] "21Q GAIN MUTATION ANALYSIS"
[1] 3
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                152 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                10                152 
[1] "22Q GAIN MUTATION ANALYSIS"
[1] 3
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                153 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                153 
[1] "XQ GAIN MUTATION ANALYSIS"
[1] 3
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               130 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               32               130 
[1] "1P LOSS MUTATION ANALYSIS"
[1] 3
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               44               118 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               44               118 
[1] "1Q LOSS MUTATION ANALYSIS"
[1] 3
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               137 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               25               137 
[1] "2P LOSS MUTATION ANALYSIS"
[1] 3
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               151 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
               11               151 
[1] "2Q LOSS MUTATION ANALYSIS"
[1] 3
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               156 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                6               156 
[1] "3P LOSS MUTATION ANALYSIS"
[1] 3
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               147 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               15               147 
[1] "3Q LOSS MUTATION ANALYSIS"
[1] 3
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               152 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
               10               152 
[1] "4P LOSS MUTATION ANALYSIS"
[1] 3
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               104 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               58               104 
[1] "4Q LOSS MUTATION ANALYSIS"
[1] 3
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65                97 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               65                97 
[1] "5P LOSS MUTATION ANALYSIS"
[1] 3
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               26               136 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               26               136 
[1] "5Q LOSS MUTATION ANALYSIS"
[1] 3
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               40               122 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               40               122 
[1] "6P LOSS MUTATION ANALYSIS"
[1] 3
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               149 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               13               149 
[1] "6Q LOSS MUTATION ANALYSIS"
[1] 3
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               140 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               22               140 
[1] "7Q LOSS MUTATION ANALYSIS"
[1] 3
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               159 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                3               159 
[1] "8P LOSS MUTATION ANALYSIS"
[1] 3
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               75                87 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               75                87 
[1] "8Q LOSS MUTATION ANALYSIS"
[1] 3
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               151 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               11               151 
[1] "9P LOSS MUTATION ANALYSIS"
[1] 3
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               22               140 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               22               140 
[1] "9Q LOSS MUTATION ANALYSIS"
[1] 3
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22               140 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               22               140 
[1] "10P LOSS MUTATION ANALYSIS"
[1] 3
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                130 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                32                130 
[1] "10Q LOSS MUTATION ANALYSIS"
[1] 3
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                125 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                37                125 
[1] "11P LOSS MUTATION ANALYSIS"
[1] 3
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                138 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                24                138 
[1] "11Q LOSS MUTATION ANALYSIS"
[1] 3
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                132 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                30                132 
[1] "12P LOSS MUTATION ANALYSIS"
[1] 3
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                140 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                22                140 
[1] "12Q LOSS MUTATION ANALYSIS"
[1] 3
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                142 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                20                142 
[1] "13Q LOSS MUTATION ANALYSIS"
[1] 3
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 8                154 
[1] "14Q LOSS MUTATION ANALYSIS"
[1] 3
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                65                 97 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                65                 97 
[1] "15Q LOSS MUTATION ANALYSIS"
[1] 3
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                72                 90 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                72                 90 
[1] "16P LOSS MUTATION ANALYSIS"
[1] 3
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 9                153 
[1] "16Q LOSS MUTATION ANALYSIS"
[1] 3
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                148 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                14                148 
[1] "17P LOSS MUTATION ANALYSIS"
[1] 3
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               104                 58 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
               104                 58 
[1] "17Q LOSS MUTATION ANALYSIS"
[1] 3
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                137 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                25                137 
[1] "18P LOSS MUTATION ANALYSIS"
[1] 3
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               125                 37 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               125                 37 
[1] "18Q LOSS MUTATION ANALYSIS"
[1] 3
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               135                 27 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               135                 27 
[1] "19P LOSS MUTATION ANALYSIS"
[1] 3
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                140 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                22                140 
[1] "19Q LOSS MUTATION ANALYSIS"
[1] 3
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                141 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                21                141 
[1] "20P LOSS MUTATION ANALYSIS"
[1] 3
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                137 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                25                137 
[1] "21Q LOSS MUTATION ANALYSIS"
[1] 3
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                66                 96 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                66                 96 
[1] "22Q LOSS MUTATION ANALYSIS"
[1] 3
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                105 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                57                105 
[1] "XQ LOSS MUTATION ANALYSIS"
[1] 3
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               25               137 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               25               137 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 162 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         734          546          524         1309          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
         387         1148           NA          441          257          468 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
         609          316           NA          365          974          244 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
         215           31           61           NA           31         1400 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          NA           NA         1035           NA         1522          366 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
         184           NA           NA           30          485          608 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
          NA          608           NA          243           30          912 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
          31         1003           30           30           NA          608 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
          31           NA         1124          518          396         1065 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
         426           31         1461           NA          974          608 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 
         853         1096          427           31          518           NA 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
          NA           30          638          424          183          790 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
         700         1126          485         1096          276           31 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
         365          943         2130         1947          334           NA 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1520           NA           NA         1885         1247         1157 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
          15           44           21           22          140           55 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
         310          184          184           NA          212          285 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
         144          425         1826          243          334          335 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
         457          395          365          425          457         1095 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
         216          914          394          397          306          161 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        3846         1258         1741         3932          734         1566 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
         992           15           73          625          607          636 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
         517          556          482          538          497          496 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
         499          262          350          328          415          531 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
         364          257           NA         1141          952          452 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
          12           31           20           21           16           34 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          23           14           NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 162 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  29 109  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  29 109  14 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  29 109  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  29 109  14 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
83 45 32 
[1] "table(vv)"
vv
N0 N1 N2 
83 45 32 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
83 45 32 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
83 45 32 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=17, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 1P GAIN MUTATION ANALYSIS
D1V1, survival
                   sevent
clus2                 0   1
  1P GAIN MUTATED     7   3
  1P GAIN WILD-TYPE 121  19
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
               10               140 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
                3                19 
$`1P GAIN MUTATED`
TCGA-AF-2692 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-A026 TCGA-DC-6156 TCGA-DY-A1DF 
       13.55        32.02        46.03         1.94        15.02        24.13 
TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 TCGA-G5-6641 
       10.78         8.45         9.96        26.43 

$`1P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  1P GAIN MUTATED 1P GAIN WILD-TYPE 
             1.94              0.39 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
            46.03            129.27 
  1P GAIN MUTATED 1P GAIN WILD-TYPE 
           14.285            14.270 
[1] "1.9 - 46.0 (14.3)"  "0.4 - 129.3 (14.3)"
[1] "hr=" "2.7"
D1V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P GAIN MUTATED         1        1         4         0         0         0
  1P GAIN WILD-TYPE      29        7        34         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P GAIN MUTATED            2          0          2        0         2
  1P GAIN WILD-TYPE          7         23         12       18         7
D1V3, multiclass
            clus
vv           1P GAIN MUTATED 1P GAIN WILD-TYPE
  STAGE I                  1                29
  STAGE II                 1                 7
  STAGE IIA                4                34
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               2                 7
  STAGE IIIB               0                23
  STAGE IIIC               2                12
  STAGE IV                 0                18
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  1P GAIN MUTATED     1   1   6   4
  1P GAIN WILD-TYPE   8  28 103  10
D1V4, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  T1               1                 8
  T2               1                28
  T3               6               103
  T4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1P GAIN MUTATED    6  2  4
  1P GAIN WILD-TYPE 77 43 28
D1V5, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  N0               6                77
  N1               2                43
  N2               4                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1P GAIN MUTATED    10   0   1   1
  1P GAIN WILD-TYPE 113  22   1  12
D1V6, multiclass
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  M0               10               113
  M1                0                22
  M1A               1                 1
  MX                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                   cls
clus                 0  1
  1P GAIN MUTATED    6  6
  1P GAIN WILD-TYPE 68 82
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      6    6
  1P GAIN WILD-TYPE   68   82
        clus
vv       1P GAIN MUTATED 1P GAIN WILD-TYPE
  FEMALE               6                68
  MALE                 6                82
[1] 2 2
[1] FALSE
D1V8, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     8   3
  1P GAIN WILD-TYPE 135  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      8    3
  1P GAIN WILD-TYPE  135   10
                                clus
vv                               1P GAIN MUTATED 1P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        8               135
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D1V9, binary
                   cls
clus                  0   1
  1P GAIN MUTATED     0  12
  1P GAIN WILD-TYPE   6 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P GAIN MUTATED      0   12
  1P GAIN WILD-TYPE    6  144
     clus
vv    1P GAIN MUTATED 1P GAIN WILD-TYPE
  NO                0                 6
  YES              12               144
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1P GAIN MUTATED    10   1   0   0
  1P GAIN WILD-TYPE 111   1  12   3
D1V10, multiclass
    clus
vv   1P GAIN MUTATED 1P GAIN WILD-TYPE
  R0              10               111
  R1               1                 1
  R2               0                12
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P GAIN MUTATED       0                         0     7
  1P GAIN WILD-TYPE     1                         3    74
D1V12, multiclass
                           clus
vv                          1P GAIN MUTATED 1P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   7                74
[1] 3 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    25   4
  1Q GAIN WILD-TYPE 103  18
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
               29               121 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
                4                18 
$`1Q GAIN MUTATED`
TCGA-AF-2692 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 
       13.55        15.39        10.39        32.02        46.03        34.03 
TCGA-AG-3600 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A026 
        6.05        36.03        31.00        70.03        51.98         1.94 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6155 
       38.04         0.49         0.69         0.72         9.37        13.97 
TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       15.02       129.27        24.13         8.61        10.78        13.64 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6641 
        8.45         9.96         0.69         0.76        26.43 

$`1Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 
       37.74        10.39        14.50         8.45        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        1.02         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        49.97        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        1.45         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02        12.99        12.00        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       41.36        57.24        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 
       17.69        16.34        16.31        16.41        11.51        17.46 
TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.53         1.12         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
             0.49              0.39 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
           129.27            126.44 
  1Q GAIN MUTATED 1Q GAIN WILD-TYPE 
            13.64             14.86 
[1] "0.5 - 129.3 (13.6)" "0.4 - 126.4 (14.9)"
[1] "hr=" "1.3"
D2V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q GAIN MUTATED         3        2         8         0         0         0
  1Q GAIN WILD-TYPE      27        6        30         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q GAIN MUTATED            3          3          5        4         2
  1Q GAIN WILD-TYPE          6         20          9       14         7
D2V3, multiclass
            clus
vv           1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  STAGE I                  3                27
  STAGE II                 2                 6
  STAGE IIA                8                30
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               3                 6
  STAGE IIIB               3                20
  STAGE IIIC               5                 9
  STAGE IV                 4                14
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q GAIN MUTATED    3  3 18  8
  1Q GAIN WILD-TYPE  6 26 91  6
D2V4, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  T1               3                 6
  T2               3                26
  T3              18                91
  T4               8                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1Q GAIN MUTATED   14  8  9
  1Q GAIN WILD-TYPE 69 37 23
D2V5, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  N0              14                69
  N1               8                37
  N2               9                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1Q GAIN MUTATED    23   4   1   4
  1Q GAIN WILD-TYPE 100  18   1   9
D2V6, multiclass
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  M0               23               100
  M1                4                18
  M1A               1                 1
  MX                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                   cls
clus                 0  1
  1Q GAIN MUTATED   17 15
  1Q GAIN WILD-TYPE 57 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     17   15
  1Q GAIN WILD-TYPE   57   73
        clus
vv       1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  FEMALE              17                57
  MALE                15                73
[1] 2 2
[1] FALSE
D2V8, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED    26   4
  1Q GAIN WILD-TYPE 117   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED     26    4
  1Q GAIN WILD-TYPE  117    9
                                clus
vv                               1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       26               117
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
D2V9, binary
                   cls
clus                  0   1
  1Q GAIN MUTATED     2  30
  1Q GAIN WILD-TYPE   4 126
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q GAIN MUTATED      2   30
  1Q GAIN WILD-TYPE    4  126
     clus
vv    1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  NO                2                 4
  YES              30               126
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q GAIN MUTATED    21   1   2   0
  1Q GAIN WILD-TYPE 100   1  10   3
D2V10, multiclass
    clus
vv   1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  R0              21               100
  R1               1                 1
  R2               2                10
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q GAIN MUTATED       0                         0    19
  1Q GAIN WILD-TYPE     1                         3    62
D2V12, multiclass
                           clus
vv                          1Q GAIN MUTATED 1Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                  19                62
[1] 3 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   29  8
  2P GAIN WILD-TYPE 99 14
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
               37               113 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
                8                14 
$`2P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3587 
       24.13        17.95        17.23         8.45        36.03        46.03 
TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 
       34.03        19.99        19.99         1.02         1.02         0.99 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 TCGA-BM-6198 
       12.00        31.00        70.03        38.04         4.60        10.19 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       60.03         7.99        10.98        12.99        12.00        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6514 
       36.00        13.05       129.27        51.48        20.55        16.31 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
       13.64         9.96        37.51         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

$`2P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       14.50        15.39        20.02        10.39        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        1.02        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 
        4.73        13.97        11.01        15.02        13.97         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       57.24        24.13        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6641 
        0.69         0.53         1.12         0.76        26.43 

  2P GAIN MUTATED 2P GAIN WILD-TYPE 
             0.46              0.39 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
           129.27            126.44 
  2P GAIN MUTATED 2P GAIN WILD-TYPE 
            17.95             13.97 
[1] "0.5 - 129.3 (17.9)" "0.4 - 126.4 (14.0)"
[1] "hr=" "1.1"
D3V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P GAIN MUTATED         6        3         8         0         1         1
  2P GAIN WILD-TYPE      24        5        30         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P GAIN MUTATED            0          6          6        4         3
  2P GAIN WILD-TYPE          9         17          8       14         6
D3V3, multiclass
            clus
vv           2P GAIN MUTATED 2P GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA                8                30
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                1                 4
  STAGE IIIA               0                 9
  STAGE IIIB               6                17
  STAGE IIIC               6                 8
  STAGE IV                 4                14
  STAGE IVA                3                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P GAIN MUTATED    0  7 27  4
  2P GAIN WILD-TYPE  9 22 82 10
D3V4, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  T1               0                 9
  T2               7                22
  T3              27                82
  T4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2P GAIN MUTATED   18  9 11
  2P GAIN WILD-TYPE 65 36 21
D3V5, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  N0              18                65
  N1               9                36
  N2              11                21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  2P GAIN MUTATED   26  6   1  4
  2P GAIN WILD-TYPE 97 16   1  9
D3V6, multiclass
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  M0               26                97
  M1                6                16
  M1A               1                 1
  MX                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                   cls
clus                 0  1
  2P GAIN MUTATED   24 15
  2P GAIN WILD-TYPE 50 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     24   15
  2P GAIN WILD-TYPE   50   73
        clus
vv       2P GAIN MUTATED 2P GAIN WILD-TYPE
  FEMALE              24                50
  MALE                15                73
[1] 2 2
[1] FALSE
D3V8, binary
                   cls
clus                  0   1
  2P GAIN MUTATED    39   0
  2P GAIN WILD-TYPE 104  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED     39    0
  2P GAIN WILD-TYPE  104   13
                                clus
vv                               2P GAIN MUTATED 2P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       39               104
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D3V9, binary
                   cls
clus                  0   1
  2P GAIN MUTATED     2  37
  2P GAIN WILD-TYPE   4 119
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P GAIN MUTATED      2   37
  2P GAIN WILD-TYPE    4  119
     clus
vv    2P GAIN MUTATED 2P GAIN WILD-TYPE
  NO                2                 4
  YES              37               119
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2P GAIN MUTATED   30  1  2  2
  2P GAIN WILD-TYPE 91  1 10  1
D3V10, multiclass
    clus
vv   2P GAIN MUTATED 2P GAIN WILD-TYPE
  R0              30                91
  R1               1                 1
  R2               2                10
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P GAIN MUTATED       0                         2    24
  2P GAIN WILD-TYPE     1                         1    57
D3V12, multiclass
                           clus
vv                          2P GAIN MUTATED 2P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  24                57
[1] 3 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   31  8
  2Q GAIN WILD-TYPE 97 14
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
               39               111 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
                8                14 
$`2Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       24.13        17.95        17.23        10.39         8.45        15.39 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3896 
       36.03        46.03        34.03        19.99        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L TCGA-AG-A01N 
       48.03        28.04         1.02         0.99        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A032 TCGA-AH-6897 TCGA-BM-6198 TCGA-CL-5917 TCGA-CL-5918 
       70.03        38.04         4.60        10.19        60.03         7.99 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE 
       12.99        12.00        15.02        36.00        13.05       129.27 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6863 
        2.40        16.31        13.64         9.96        37.51         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.46        18.28        47.08 

$`2Q GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        19.10        12.72        37.74        14.50 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        1.02         2.01        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       32.02        19.99        36.03        14.04        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07         1.02        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        1.45         0.69         0.72         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
        6.97         9.37         4.73        13.97        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        13.97         7.10        30.05        12.95        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       11.51        10.78        17.46        11.97         8.45        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6641 
        1.12        55.76        26.43 

  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
             0.46              0.39 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
           129.27            126.44 
  2Q GAIN MUTATED 2Q GAIN WILD-TYPE 
            16.31             13.97 
[1] "0.5 - 129.3 (16.3)" "0.4 - 126.4 (14.0)"
[1] "hr=" "1.3"
D4V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q GAIN MUTATED         6        3         9         0         1         1
  2Q GAIN WILD-TYPE      24        5        29         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q GAIN MUTATED            0          6          7        5         2
  2Q GAIN WILD-TYPE          9         17          7       13         7
D4V3, multiclass
            clus
vv           2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA                9                29
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                1                 4
  STAGE IIIA               0                 9
  STAGE IIIB               6                17
  STAGE IIIC               7                 7
  STAGE IV                 5                13
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2Q GAIN MUTATED    0  7 28  5
  2Q GAIN WILD-TYPE  9 22 81  9
D4V4, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  T1               0                 9
  T2               7                22
  T3              28                81
  T4               5                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2Q GAIN MUTATED   19  9 12
  2Q GAIN WILD-TYPE 64 36 20
D4V5, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  N0              19                64
  N1               9                36
  N2              12                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  2Q GAIN MUTATED   28  6   1  4
  2Q GAIN WILD-TYPE 95 16   1  9
D4V6, multiclass
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  M0               28                95
  M1                6                16
  M1A               1                 1
  MX                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                   cls
clus                 0  1
  2Q GAIN MUTATED   25 16
  2Q GAIN WILD-TYPE 49 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     25   16
  2Q GAIN WILD-TYPE   49   72
        clus
vv       2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  FEMALE              25                49
  MALE                16                72
[1] 2 2
[1] FALSE
D4V8, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED    41   0
  2Q GAIN WILD-TYPE 102  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED     41    0
  2Q GAIN WILD-TYPE  102   13
                                clus
vv                               2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       41               102
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D4V9, binary
                   cls
clus                  0   1
  2Q GAIN MUTATED     3  38
  2Q GAIN WILD-TYPE   3 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q GAIN MUTATED      3   38
  2Q GAIN WILD-TYPE    3  118
     clus
vv    2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  NO                3                 3
  YES              38               118
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  2Q GAIN MUTATED   33  0  2  2
  2Q GAIN WILD-TYPE 88  2 10  1
D4V10, multiclass
    clus
vv   2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  R0              33                88
  R1               0                 2
  R2               2                10
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q GAIN MUTATED       0                         3    23
  2Q GAIN WILD-TYPE     1                         0    58
D4V12, multiclass
                           clus
vv                          2Q GAIN MUTATED 2Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               3                 0
  WHITE                                  23                58
[1] 3 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    21   2
  3P GAIN WILD-TYPE 107  20
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
               23               127 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
                2                20 
$`3P GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3593 TCGA-AG-3612 TCGA-AG-3896 
       37.74        20.02        10.39        34.03        19.99         1.02 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A020 TCGA-CI-6623 
       36.03        14.04         9.07        12.00        10.98         9.37 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE 
       10.98        12.99        15.02        12.95        41.36       129.27 
TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
        2.40        18.28        11.97        14.86         1.02 

$`3P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3574 
       12.72        10.39        14.50         8.45        15.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        19.99        28.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95        36.03         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       12.00        13.97        36.00         7.10        30.05        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29       126.44        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       37.51        31.30         0.39         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  3P GAIN MUTATED 3P GAIN WILD-TYPE 
             1.02              0.39 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
           129.27            126.44 
  3P GAIN MUTATED 3P GAIN WILD-TYPE 
            12.99             15.02 
[1] "1.0 - 129.3 (13.0)" "0.4 - 126.4 (15.0)"
[1] "hr=" "1.7"
D5V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P GAIN MUTATED         2        0         9         0         0         2
  3P GAIN WILD-TYPE      28        8        29         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P GAIN MUTATED            1          4          1        4         4
  3P GAIN WILD-TYPE          8         19         13       14         5
D5V3, multiclass
            clus
vv           3P GAIN MUTATED 3P GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 0                 8
  STAGE IIA                9                29
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                2                 3
  STAGE IIIA               1                 8
  STAGE IIIB               4                19
  STAGE IIIC               1                13
  STAGE IV                 4                14
  STAGE IVA                4                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P GAIN MUTATED    1  3 21  2
  3P GAIN WILD-TYPE  8 26 88 12
D5V4, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              21                88
  T4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3P GAIN MUTATED   12  7  8
  3P GAIN WILD-TYPE 71 38 24
D5V5, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  N0              12                71
  N1               7                38
  N2               8                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3P GAIN MUTATED    18   4   2   3
  3P GAIN WILD-TYPE 105  18   0  10
D5V6, multiclass
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  M0               18               105
  M1                4                18
  M1A               2                 0
  MX                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                   cls
clus                 0  1
  3P GAIN MUTATED   14 13
  3P GAIN WILD-TYPE 60 75
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     14   13
  3P GAIN WILD-TYPE   60   75
        clus
vv       3P GAIN MUTATED 3P GAIN WILD-TYPE
  FEMALE              14                60
  MALE                13                75
[1] 2 2
[1] FALSE
D5V8, binary
                   cls
clus                  0   1
  3P GAIN MUTATED    26   1
  3P GAIN WILD-TYPE 117  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED     26    1
  3P GAIN WILD-TYPE  117   12
                                clus
vv                               3P GAIN MUTATED 3P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       26               117
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D5V9, binary
                   cls
clus                  0   1
  3P GAIN MUTATED     2  25
  3P GAIN WILD-TYPE   4 131
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P GAIN MUTATED      2   25
  3P GAIN WILD-TYPE    4  131
     clus
vv    3P GAIN MUTATED 3P GAIN WILD-TYPE
  NO                2                 4
  YES              25               131
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P GAIN MUTATED    20   0   1   0
  3P GAIN WILD-TYPE 101   2  11   3
D5V10, multiclass
    clus
vv   3P GAIN MUTATED 3P GAIN WILD-TYPE
  R0              20               101
  R1               0                 2
  R2               1                11
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P GAIN MUTATED       0                         1    14
  3P GAIN WILD-TYPE     1                         2    67
D5V12, multiclass
                           clus
vv                          3P GAIN MUTATED 3P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                  14                67
[1] 3 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    26   3
  3Q GAIN WILD-TYPE 102  19
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
               29               121 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
                3                19 
$`3Q GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3593 TCGA-AG-3612 
       37.74        10.39        20.02        10.39        34.03        19.99 
TCGA-AG-3726 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A016 TCGA-AG-A01L 
        7.99         1.02        36.03        14.04         9.07        12.00 
TCGA-AG-A020 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6156 
       10.98         9.37        60.03        10.98        12.99        15.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DC TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 
       12.95        13.05        41.36         2.40        18.28        16.31 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       11.97        14.86         0.39         1.02         0.76 

$`3Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3575 
       12.72        14.50         8.45        15.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        19.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
       36.03         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
        7.99        11.01        15.02        12.00        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
        7.10        30.05        10.06         5.29       126.44        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 
        8.45         9.96        37.51        31.30         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
             0.39              0.46 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            60.03            129.27 
  3Q GAIN MUTATED 3Q GAIN WILD-TYPE 
            12.95             15.85 
[1] "0.4 - 60.0 (12.9)"  "0.5 - 129.3 (15.8)"
[1] "hr=" "1.2"
D6V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q GAIN MUTATED         3        0        11         0         0         2
  3Q GAIN WILD-TYPE      27        8        27         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q GAIN MUTATED            1          6          2        5         4
  3Q GAIN WILD-TYPE          8         17         12       13         5
D6V3, multiclass
            clus
vv           3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  STAGE I                  3                27
  STAGE II                 0                 8
  STAGE IIA               11                27
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                2                 3
  STAGE IIIA               1                 8
  STAGE IIIB               6                17
  STAGE IIIC               2                12
  STAGE IV                 5                13
  STAGE IVA                4                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3Q GAIN MUTATED    1  4 26  3
  3Q GAIN WILD-TYPE  8 25 83 11
D6V4, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  T1               1                 8
  T2               4                25
  T3              26                83
  T4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3Q GAIN MUTATED   15 10  9
  3Q GAIN WILD-TYPE 68 35 23
D6V5, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  N0              15                68
  N1              10                35
  N2               9                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3Q GAIN MUTATED    23   5   2   4
  3Q GAIN WILD-TYPE 100  17   0   9
D6V6, multiclass
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  M0               23               100
  M1                5                17
  M1A               2                 0
  MX                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                   cls
clus                 0  1
  3Q GAIN MUTATED   18 16
  3Q GAIN WILD-TYPE 56 72
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     18   16
  3Q GAIN WILD-TYPE   56   72
        clus
vv       3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  FEMALE              18                56
  MALE                16                72
[1] 2 2
[1] FALSE
D6V8, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED    33   1
  3Q GAIN WILD-TYPE 110  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED     33    1
  3Q GAIN WILD-TYPE  110   12
                                clus
vv                               3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       33               110
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D6V9, binary
                   cls
clus                  0   1
  3Q GAIN MUTATED     2  32
  3Q GAIN WILD-TYPE   4 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q GAIN MUTATED      2   32
  3Q GAIN WILD-TYPE    4  124
     clus
vv    3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  NO                2                 4
  YES              32               124
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  3Q GAIN MUTATED   27  0  1  1
  3Q GAIN WILD-TYPE 94  2 11  2
D6V10, multiclass
    clus
vv   3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  R0              27                94
  R1               0                 2
  R2               1                11
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q GAIN MUTATED       0                         2    18
  3Q GAIN WILD-TYPE     1                         1    63
D6V12, multiclass
                           clus
vv                          3Q GAIN MUTATED 3Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  18                63
[1] 3 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     7   1
  4P GAIN WILD-TYPE 121  21
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                8               142 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
                1                21 
$`4P GAIN MUTATED`
TCGA-AG-3890 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A011 TCGA-DC-4749 TCGA-DC-6682 
       17.03        32.02         0.99        37.02        11.01        13.05 
TCGA-DY-A1DG TCGA-EI-6510 
       51.48        18.28 

$`4P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       20.98        13.94         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  4P GAIN MUTATED 4P GAIN WILD-TYPE 
             0.99              0.39 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
            51.48            129.27 
  4P GAIN MUTATED 4P GAIN WILD-TYPE 
           17.655            14.025 
[1] "1.0 - 51.5 (17.7)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.3"
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P GAIN MUTATED         2        1         3         0         0         1
  4P GAIN WILD-TYPE      28        7        35         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P GAIN MUTATED            0          0          0        0         2
  4P GAIN WILD-TYPE          9         23         14       18         7
D7V3, multiclass
            clus
vv           4P GAIN MUTATED 4P GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 1                 7
  STAGE IIA                3                35
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                1                 4
  STAGE IIIA               0                 9
  STAGE IIIB               0                23
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4P GAIN MUTATED     0   3   6   0
  4P GAIN WILD-TYPE   9  26 103  14
D7V4, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  T1               0                 9
  T2               3                26
  T3               6               103
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  4P GAIN MUTATED    7  2  0
  4P GAIN WILD-TYPE 76 43 32
D7V5, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  N0               7                76
  N1               2                43
  N2               0                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  4P GAIN MUTATED     6   1   0   2
  4P GAIN WILD-TYPE 117  21   2  11
D7V6, multiclass
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  M0                6               117
  M1                1                21
  M1A               0                 2
  MX                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                   cls
clus                 0  1
  4P GAIN MUTATED    2  7
  4P GAIN WILD-TYPE 72 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      2    7
  4P GAIN WILD-TYPE   72   81
        clus
vv       4P GAIN MUTATED 4P GAIN WILD-TYPE
  FEMALE               2                72
  MALE                 7                81
[1] 2 2
[1] FALSE
D7V8, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     9   0
  4P GAIN WILD-TYPE 134  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      9    0
  4P GAIN WILD-TYPE  134   13
                                clus
vv                               4P GAIN MUTATED 4P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               134
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D7V9, binary
                   cls
clus                  0   1
  4P GAIN MUTATED     0   9
  4P GAIN WILD-TYPE   6 147
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P GAIN MUTATED      0    9
  4P GAIN WILD-TYPE    6  147
     clus
vv    4P GAIN MUTATED 4P GAIN WILD-TYPE
  NO                0                 6
  YES               9               147
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4P GAIN MUTATED     7   0   0   0
  4P GAIN WILD-TYPE 114   2  12   3
D7V10, multiclass
    clus
vv   4P GAIN MUTATED 4P GAIN WILD-TYPE
  R0               7               114
  R1               0                 2
  R2               0                12
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P GAIN MUTATED       0                         0     5
  4P GAIN WILD-TYPE     1                         3    76
D7V12, multiclass
                           clus
vv                          4P GAIN MUTATED 4P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   5                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(8) Variable = 4Q GAIN MUTATION ANALYSIS
D8V1, survival
                   sevent
clus2                 0   1
  4Q GAIN MUTATED     4   1
  4Q GAIN WILD-TYPE 124  21
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                5               145 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                1                21 
$`4Q GAIN MUTATED`
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3902 TCGA-DC-6682 TCGA-DY-A1DG 
       17.03        35.01        32.02        13.05        51.48 

$`4Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       36.95        13.02        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            13.05              0.39 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            51.48            129.27 
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
            32.02             14.01 
[1] "13.1 - 51.5 (32.0)" "0.4 - 129.3 (14.0)"
[1] "hr=" "1.1"
D8V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q GAIN MUTATED         1        0         2         0         0         0
  4Q GAIN WILD-TYPE      29        8        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q GAIN MUTATED            0          1          0        0         1
  4Q GAIN WILD-TYPE          9         22         14       18         8
D8V3, multiclass
            clus
vv           4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                2                36
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               1                22
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  4Q GAIN MUTATED     0   1   4   0
  4Q GAIN WILD-TYPE   9  28 105  14
D8V4, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  T1               0                 9
  T2               1                28
  T3               4               105
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  4Q GAIN MUTATED    3  2  0
  4Q GAIN WILD-TYPE 80 43 32
D8V5, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  N0               3                80
  N1               2                43
  N2               0                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  4Q GAIN MUTATED     4   1   0   0
  4Q GAIN WILD-TYPE 119  21   2  13
D8V6, multiclass
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  M0                4               119
  M1                1                21
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                   cls
clus                 0  1
  4Q GAIN MUTATED    0  5
  4Q GAIN WILD-TYPE 74 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE   74   83
        clus
vv       4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  FEMALE               0                74
  MALE                 5                83
[1] 2 2
[1] FALSE
D8V8, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     5   0
  4Q GAIN WILD-TYPE 138  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      5    0
  4Q GAIN WILD-TYPE  138   13
                                clus
vv                               4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D8V9, binary
                   cls
clus                  0   1
  4Q GAIN MUTATED     0   5
  4Q GAIN WILD-TYPE   6 151
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q GAIN MUTATED      0    5
  4Q GAIN WILD-TYPE    6  151
     clus
vv    4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  NO                0                 6
  YES               5               151
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  4Q GAIN MUTATED     4   0   0   0
  4Q GAIN WILD-TYPE 117   2  12   3
D8V10, multiclass
    clus
vv   4Q GAIN MUTATED 4Q GAIN WILD-TYPE
  R0               4               117
  R1               0                 2
  R2               0                12
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q GAIN MUTATED       0                         0     2
  4Q GAIN WILD-TYPE     1                         3    79
D8V12, multiclass
[1] "Remove cluster labels:" "4Q GAIN MUTATED"       
clus
  4Q GAIN MUTATED 4Q GAIN WILD-TYPE 
                2                83 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AH-6544        TCGA-AH-6547 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-5917 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1H8 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506        TCGA-EI-6507 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510        TCGA-EI-6511 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514        TCGA-EI-6881 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884        TCGA-EI-6885 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004        TCGA-F5-6464 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702        TCGA-F5-6810 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813        TCGA-F5-6814 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864        TCGA-G5-6233 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 
       TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" "4Q GAIN WILD-TYPE" 

Clustering(9) Variable = 5P GAIN MUTATION ANALYSIS
D9V1, survival
                   sevent
clus2                 0   1
  5P GAIN MUTATED    26   6
  5P GAIN WILD-TYPE 102  16
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
               32               118 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
                6                16 
$`5P GAIN MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3609 
       37.74        20.02        10.39         1.02        46.03        19.99 
TCGA-AG-3890 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01L 
       17.03        36.03         1.02        25.97        36.03        12.00 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 
       31.00         1.94        38.96        41.00        38.04         0.69 
TCGA-AH-6644 TCGA-BM-6198 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6683 
        0.72        10.19        12.99        15.02         7.10        10.06 
TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 
        2.40        16.31        11.51         9.96        14.86         1.02 
TCGA-F5-6814 TCGA-F5-6863 
        0.53         0.76 

$`5P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3574 
       12.72        10.39        14.50         8.45        15.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 
       32.02        19.99        28.04        14.04        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97         0.49         1.45         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       60.03         7.99        10.98        11.01        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       13.97        36.00        30.05        12.95        13.05         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       10.78        13.64        17.46        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 
       31.30         0.39         0.66         0.69         1.12         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  5P GAIN MUTATED 5P GAIN WILD-TYPE 
             0.53              0.39 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
            46.03            129.27 
  5P GAIN MUTATED 5P GAIN WILD-TYPE 
           12.495            14.760 
[1] "0.5 - 46.0 (12.5)"  "0.4 - 129.3 (14.8)"
[1] "hr=" "2.1"
D9V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P GAIN MUTATED         5        1         7         0         1         0
  5P GAIN WILD-TYPE      25        7        31         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P GAIN MUTATED            1          7          4        5         2
  5P GAIN WILD-TYPE          8         16         10       13         7
D9V3, multiclass
            clus
vv           5P GAIN MUTATED 5P GAIN WILD-TYPE
  STAGE I                  5                25
  STAGE II                 1                 7
  STAGE IIA                7                31
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                0                 5
  STAGE IIIA               1                 8
  STAGE IIIB               7                16
  STAGE IIIC               4                10
  STAGE IV                 5                13
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P GAIN MUTATED    1  8 19  6
  5P GAIN WILD-TYPE  8 21 90  8
D9V4, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  T1               1                 8
  T2               8                21
  T3              19                90
  T4               6                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5P GAIN MUTATED   15 11  7
  5P GAIN WILD-TYPE 68 34 25
D9V5, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  N0              15                68
  N1              11                34
  N2               7                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  5P GAIN MUTATED   24  5   1  3
  5P GAIN WILD-TYPE 99 17   1 10
D9V6, multiclass
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  M0               24                99
  M1                5                17
  M1A               1                 1
  MX                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                   cls
clus                 0  1
  5P GAIN MUTATED   11 23
  5P GAIN WILD-TYPE 63 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     11   23
  5P GAIN WILD-TYPE   63   65
        clus
vv       5P GAIN MUTATED 5P GAIN WILD-TYPE
  FEMALE              11                63
  MALE                23                65
[1] 2 2
[1] FALSE
D9V8, binary
                   cls
clus                  0   1
  5P GAIN MUTATED    34   0
  5P GAIN WILD-TYPE 109  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED     34    0
  5P GAIN WILD-TYPE  109   13
                                clus
vv                               5P GAIN MUTATED 5P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       34               109
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D9V9, binary
                   cls
clus                  0   1
  5P GAIN MUTATED     3  31
  5P GAIN WILD-TYPE   3 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P GAIN MUTATED      3   31
  5P GAIN WILD-TYPE    3  125
     clus
vv    5P GAIN MUTATED 5P GAIN WILD-TYPE
  NO                3                 3
  YES              31               125
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5P GAIN MUTATED   25  1  4  0
  5P GAIN WILD-TYPE 96  1  8  3
D9V10, multiclass
    clus
vv   5P GAIN MUTATED 5P GAIN WILD-TYPE
  R0              25                96
  R1               1                 1
  R2               4                 8
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P GAIN MUTATED       0                         1    17
  5P GAIN WILD-TYPE     1                         2    64
D9V12, multiclass
                           clus
vv                          5P GAIN MUTATED 5P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                  17                64
[1] 3 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    18   2
  5Q GAIN WILD-TYPE 110  20
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
               20               130 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
                2                20 
$`5Q GAIN MUTATED`
TCGA-AF-6655 TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3890 TCGA-AG-4007 TCGA-AG-A00H 
       20.02         1.02        19.99        17.03         1.02        25.97 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 
       12.00        31.00        41.00        38.04         0.69         0.72 
TCGA-DC-5869 TCGA-DC-6683 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6464 
       12.99        10.06        16.31        11.51        11.97         9.96 
TCGA-F5-6811 TCGA-F5-6814 
        1.02         0.53 

$`5Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03        14.04        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 
        1.94        38.96        61.97         0.49         1.45         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       15.85        17.69        16.34        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.64        17.46         8.45        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.39         0.66         0.69         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
             0.53              0.39 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
            41.00            129.27 
  5Q GAIN MUTATED 5Q GAIN WILD-TYPE 
           11.985            14.940 
[1] "0.5 - 41.0 (12.0)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "1.1"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q GAIN MUTATED         2        0         5         0         1         0
  5Q GAIN WILD-TYPE      28        8        33         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q GAIN MUTATED            1          5          3        4         0
  5Q GAIN WILD-TYPE          8         18         11       14         9
D10V3, multiclass
            clus
vv           5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 0                 8
  STAGE IIA                5                33
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                0                 5
  STAGE IIIA               1                 8
  STAGE IIIB               5                18
  STAGE IIIC               3                11
  STAGE IV                 4                14
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q GAIN MUTATED    0  5 15  2
  5Q GAIN WILD-TYPE  9 24 94 12
D10V4, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  T1               0                 9
  T2               5                24
  T3              15                94
  T4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5Q GAIN MUTATED    9  7  5
  5Q GAIN WILD-TYPE 74 38 27
D10V5, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  N0               9                74
  N1               7                38
  N2               5                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5Q GAIN MUTATED    17   4   0   1
  5Q GAIN WILD-TYPE 106  18   2  12
D10V6, multiclass
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  M0               17               106
  M1                4                18
  M1A               0                 2
  MX                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                   cls
clus                 0  1
  5Q GAIN MUTATED    8 14
  5Q GAIN WILD-TYPE 66 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      8   14
  5Q GAIN WILD-TYPE   66   74
        clus
vv       5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  FEMALE               8                66
  MALE                14                74
[1] 2 2
[1] FALSE
D10V8, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED    22   0
  5Q GAIN WILD-TYPE 121  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED     22    0
  5Q GAIN WILD-TYPE  121   13
                                clus
vv                               5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       22               121
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D10V9, binary
                   cls
clus                  0   1
  5Q GAIN MUTATED     0  22
  5Q GAIN WILD-TYPE   6 134
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q GAIN MUTATED      0   22
  5Q GAIN WILD-TYPE    6  134
     clus
vv    5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  NO                0                 6
  YES              22               134
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5Q GAIN MUTATED    17   0   3   0
  5Q GAIN WILD-TYPE 104   2   9   3
D10V10, multiclass
    clus
vv   5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  R0              17               104
  R1               0                 2
  R2               3                 9
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q GAIN MUTATED       0                         1    10
  5Q GAIN WILD-TYPE     1                         2    71
D10V12, multiclass
                           clus
vv                          5Q GAIN MUTATED 5Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                  10                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(11) Variable = 6P GAIN MUTATION ANALYSIS
D11V1, survival
                   sevent
clus2                0  1
  6P GAIN MUTATED   32  3
  6P GAIN WILD-TYPE 96 19
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
               35               115 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
                3                19 
$`6P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       24.13        43.04        37.74        10.39        14.50        15.39 
TCGA-AG-3587 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 
       46.03        19.99        29.98         1.02         1.02        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
        1.02         0.99        36.03         9.07        12.00        31.00 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 
        0.72        10.19         6.05         9.37        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 
       15.02        36.00       129.27        20.55        15.85        17.69 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 TCGA-G5-6641 
       37.51        14.86         0.39        18.28        26.43 

$`6P GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       17.95        17.23        13.55        19.10        12.72         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
        7.07         1.02         2.01        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       37.02        15.95         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04         0.49         1.45         0.69         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
       10.98        11.01        15.02        13.97         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        31.30         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 
       47.08 

  6P GAIN MUTATED 6P GAIN WILD-TYPE 
             0.39              0.46 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
           129.27            126.44 
  6P GAIN MUTATED 6P GAIN WILD-TYPE 
            15.02             13.97 
[1] "0.4 - 129.3 (15.0)" "0.5 - 126.4 (14.0)"
[1] "hr=" "1.7"
D11V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P GAIN MUTATED         7        1         5         0         1         1
  6P GAIN WILD-TYPE      23        7        33         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P GAIN MUTATED            1          9          3        7         4
  6P GAIN WILD-TYPE          8         14         11       11         5
D11V3, multiclass
            clus
vv           6P GAIN MUTATED 6P GAIN WILD-TYPE
  STAGE I                  7                23
  STAGE II                 1                 7
  STAGE IIA                5                33
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                1                 4
  STAGE IIIA               1                 8
  STAGE IIIB               9                14
  STAGE IIIC               3                11
  STAGE IV                 7                11
  STAGE IVA                4                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P GAIN MUTATED    4  5 26  5
  6P GAIN WILD-TYPE  5 24 83  9
D11V4, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  T1               4                 5
  T2               5                24
  T3              26                83
  T4               5                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6P GAIN MUTATED   14 13 12
  6P GAIN WILD-TYPE 69 32 20
D11V5, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  N0              14                69
  N1              13                32
  N2              12                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  6P GAIN MUTATED   24  9   1  5
  6P GAIN WILD-TYPE 99 13   1  8
D11V6, multiclass
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  M0               24                99
  M1                9                13
  M1A               1                 1
  MX                5                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                   cls
clus                 0  1
  6P GAIN MUTATED   16 24
  6P GAIN WILD-TYPE 58 64
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     16   24
  6P GAIN WILD-TYPE   58   64
        clus
vv       6P GAIN MUTATED 6P GAIN WILD-TYPE
  FEMALE              16                58
  MALE                24                64
[1] 2 2
[1] FALSE
D11V8, binary
                   cls
clus                  0   1
  6P GAIN MUTATED    38   1
  6P GAIN WILD-TYPE 105  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED     38    1
  6P GAIN WILD-TYPE  105   12
                                clus
vv                               6P GAIN MUTATED 6P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       38               105
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D11V9, binary
                   cls
clus                  0   1
  6P GAIN MUTATED     4  36
  6P GAIN WILD-TYPE   2 120
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P GAIN MUTATED      4   36
  6P GAIN WILD-TYPE    2  120
     clus
vv    6P GAIN MUTATED 6P GAIN WILD-TYPE
  NO                4                 2
  YES              36               120
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6P GAIN MUTATED   29  0  5  0
  6P GAIN WILD-TYPE 92  2  7  3
D11V10, multiclass
    clus
vv   6P GAIN MUTATED 6P GAIN WILD-TYPE
  R0              29                92
  R1               0                 2
  R2               5                 7
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P GAIN MUTATED       0                         3    20
  6P GAIN WILD-TYPE     1                         0    61
D11V12, multiclass
                           clus
vv                          6P GAIN MUTATED 6P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               3                 0
  WHITE                                  20                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(12) Variable = 6Q GAIN MUTATION ANALYSIS
D12V1, survival
                   sevent
clus2                 0   1
  6Q GAIN MUTATED    28   3
  6Q GAIN WILD-TYPE 100  19
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
               31               119 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
                3                19 
$`6Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       24.13        43.04        37.74        10.39        14.50        15.39 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-4022 
       19.99        29.98         1.02         1.02         1.02         0.99 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 
       36.03         9.07        12.00        31.00         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        6.05         9.37        12.99        12.00        15.02        36.00 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 
       51.48        20.55        15.85        17.69        37.51        14.86 
TCGA-F5-6810 
        0.39 

$`6Q GAIN WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       17.95        17.23        13.55        19.10        12.72         8.45 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       15.95        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W 
       25.97        23.01        37.02        15.95         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        4.60         1.81         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 
       60.03         7.99        10.98        11.01        15.02        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 
       13.64        17.46        11.97         8.45         9.96        31.30 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
             0.39              0.46 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            51.48            129.27 
  6Q GAIN MUTATED 6Q GAIN WILD-TYPE 
            14.86             14.01 
[1] "0.4 - 51.5 (14.9)"  "0.5 - 129.3 (14.0)"
[1] "hr=" "1.3"
D12V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q GAIN MUTATED         6        1         4         0         0         1
  6Q GAIN WILD-TYPE      24        7        34         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q GAIN MUTATED            0          9          2        6         5
  6Q GAIN WILD-TYPE          9         14         12       12         4
D12V3, multiclass
            clus
vv           6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA                4                34
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                1                 4
  STAGE IIIA               0                 9
  STAGE IIIB               9                14
  STAGE IIIC               2                12
  STAGE IV                 6                12
  STAGE IVA                5                 4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q GAIN MUTATED    3  4 23  5
  6Q GAIN WILD-TYPE  6 25 86  9
D12V4, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  T1               3                 6
  T2               4                25
  T3              23                86
  T4               5                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6Q GAIN MUTATED   12 13  9
  6Q GAIN WILD-TYPE 71 32 23
D12V5, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  N0              12                71
  N1              13                32
  N2               9                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6Q GAIN MUTATED    20   9   1   4
  6Q GAIN WILD-TYPE 103  13   1   9
D12V6, multiclass
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  M0               20               103
  M1                9                13
  M1A               1                 1
  MX                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                   cls
clus                 0  1
  6Q GAIN MUTATED   14 21
  6Q GAIN WILD-TYPE 60 67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     14   21
  6Q GAIN WILD-TYPE   60   67
        clus
vv       6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  FEMALE              14                60
  MALE                21                67
[1] 2 2
[1] FALSE
D12V8, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED    34   0
  6Q GAIN WILD-TYPE 109  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED     34    0
  6Q GAIN WILD-TYPE  109   13
                                clus
vv                               6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       34               109
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D12V9, binary
                   cls
clus                  0   1
  6Q GAIN MUTATED     4  31
  6Q GAIN WILD-TYPE   2 125
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q GAIN MUTATED      4   31
  6Q GAIN WILD-TYPE    2  125
     clus
vv    6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  NO                4                 2
  YES              31               125
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  6Q GAIN MUTATED   24  0  5  0
  6Q GAIN WILD-TYPE 97  2  7  3
D12V10, multiclass
    clus
vv   6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  R0              24                97
  R1               0                 2
  R2               5                 7
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q GAIN MUTATED       0                         3    18
  6Q GAIN WILD-TYPE     1                         0    63
D12V12, multiclass
                           clus
vv                          6Q GAIN MUTATED 6Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               3                 0
  WHITE                                  18                63
[1] 3 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   77 16
  7P GAIN WILD-TYPE 51  6
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               93                57 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
               16                 6 
$`7P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       24.13        17.95        17.23        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
        8.45        15.39        20.02         7.07         1.02        24.00 
TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       46.03        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 
       19.99        29.98         0.99         0.99        19.99        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 
       35.01         1.02        48.03        19.99        36.03         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       17.03         0.99        25.97        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G 
        1.02        12.00        31.00        70.03         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
       38.04         0.49         0.69         0.72         4.60        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         9.37         4.73        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        12.99        12.00        15.02        36.00         7.10 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
       24.13         0.49         2.40        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34        16.31        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`7P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3574 
       43.04        13.55        19.10        12.72        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
       12.00        32.02         8.02         2.01         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        2.01        50.04         7.99         0.99         1.02        32.98 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 
        1.02        36.95        13.02        14.01        32.02        28.04 
TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       14.04        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 
        1.45         1.81         6.05         6.97        13.97        15.02 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A1DG TCGA-DY-A1H8 
       13.97        30.05        12.95        13.05        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
       20.55        19.96        17.00        16.41         8.61        17.46 
TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 
       37.51         0.53         1.12 

  7P GAIN MUTATED 7P GAIN WILD-TYPE 
             0.39              0.53 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
           129.27             64.01 
  7P GAIN MUTATED 7P GAIN WILD-TYPE 
            14.50             14.04 
[1] "0.4 - 129.3 (14.5)" "0.5 - 64.0 (14.0)" 
[1] "hr=" "1.8"
D13V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7P GAIN MUTATED        17        4        20         1         2         1
  7P GAIN WILD-TYPE      13        4        18         1         0         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7P GAIN MUTATED            3         20         11       12         6
  7P GAIN WILD-TYPE          6          3          3        6         3
D13V3, multiclass
            clus
vv           7P GAIN MUTATED 7P GAIN WILD-TYPE
  STAGE I                 17                13
  STAGE II                 4                 4
  STAGE IIA               20                18
  STAGE IIB                1                 1
  STAGE IIC                2                 0
  STAGE III                1                 4
  STAGE IIIA               3                 6
  STAGE IIIB              20                 3
  STAGE IIIC              11                 3
  STAGE IV                12                 6
  STAGE IVA                6                 3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7P GAIN MUTATED    4 18 66 11
  7P GAIN WILD-TYPE  5 11 43  3
D13V4, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  T1               4                 5
  T2              18                11
  T3              66                43
  T4              11                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  7P GAIN MUTATED   45 31 22
  7P GAIN WILD-TYPE 38 14 10
D13V5, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  N0              45                38
  N1              31                14
  N2              22                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  7P GAIN MUTATED   73 15   1  9
  7P GAIN WILD-TYPE 50  7   1  4
D13V6, multiclass
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  M0               73                50
  M1               15                 7
  M1A               1                 1
  MX                9                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   44 56
  7P GAIN WILD-TYPE 30 32
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     44   56
  7P GAIN WILD-TYPE   30   32
        clus
vv       7P GAIN MUTATED 7P GAIN WILD-TYPE
  FEMALE              44                30
  MALE                56                32
[1] 2 2
[1] FALSE
D13V8, binary
                   cls
clus                 0  1
  7P GAIN MUTATED   95  3
  7P GAIN WILD-TYPE 48 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED     95    3
  7P GAIN WILD-TYPE   48   10
                                clus
vv                               7P GAIN MUTATED 7P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       95                48
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D13V9, binary
                   cls
clus                 0  1
  7P GAIN MUTATED    4 96
  7P GAIN WILD-TYPE  2 60
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7P GAIN MUTATED      4   96
  7P GAIN WILD-TYPE    2   60
     clus
vv    7P GAIN MUTATED 7P GAIN WILD-TYPE
  NO                4                 2
  YES              96                60
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7P GAIN MUTATED   73  2  8  3
  7P GAIN WILD-TYPE 48  0  4  0
D13V10, multiclass
    clus
vv   7P GAIN MUTATED 7P GAIN WILD-TYPE
  R0              73                48
  R1               2                 0
  R2               8                 4
  RX               3                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7P GAIN MUTATED       1                         3    55
  7P GAIN WILD-TYPE     0                         0    26
D13V12, multiclass
                           clus
vv                          7P GAIN MUTATED 7P GAIN WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               3                 0
  WHITE                                  55                26
[1] 3 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   65 13
  7Q GAIN WILD-TYPE 63  9
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               78                72 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
               13                 9 
$`7Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       24.13        17.95        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3599 
       20.02         7.07         1.02        24.00        46.03        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 
        0.99        15.95        19.99        19.99        29.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        0.99        19.99        17.03        35.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A014 
       19.99        28.04         1.02         0.99        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.96        38.04         0.49         0.69         0.72         4.60 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       10.19         6.05         9.37        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        12.99        12.00        15.02        36.00         7.10 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 
       10.06         5.29        41.36        57.24        24.13         0.49 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 
       20.91        18.28        15.85        17.69        16.31        11.51 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         9.96        31.30        14.86         0.39         1.02 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76         0.46        55.76        47.08        26.43 

$`7Q GAIN WILD-TYPE`
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 
       10.39        36.03        12.00        32.02         8.02         2.01 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3726 
        1.02        34.03         2.01        50.04         6.05         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         1.02        32.98         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       14.01        32.02        36.03        14.04        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01Y TCGA-AG-A020 
       13.94         6.02        23.01        37.02        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       51.98        49.97         1.94        61.97        41.00         1.45 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-5337 
        1.81         6.05         6.97         4.73        13.97        15.02 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE 
       13.97        30.05        12.95        13.05       126.44       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 
       51.48        32.61         2.40        20.55        19.96        17.00 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6233 
        8.45        37.51         0.66         0.53         1.12        18.28 

  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
             0.39              0.53 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
            70.03            129.27 
  7Q GAIN MUTATED 7Q GAIN WILD-TYPE 
           14.680            14.025 
[1] "0.4 - 70.0 (14.7)"  "0.5 - 129.3 (14.0)"
[1] "hr=" "1.6"
D14V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7Q GAIN MUTATED        16        3        12         1         1         1
  7Q GAIN WILD-TYPE      14        5        26         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7Q GAIN MUTATED            2         19          9       11         5
  7Q GAIN WILD-TYPE          7          4          5        7         4
D14V3, multiclass
            clus
vv           7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  STAGE I                 16                14
  STAGE II                 3                 5
  STAGE IIA               12                26
  STAGE IIB                1                 1
  STAGE IIC                1                 1
  STAGE III                1                 4
  STAGE IIIA               2                 7
  STAGE IIIB              19                 4
  STAGE IIIC               9                 5
  STAGE IV                11                 7
  STAGE IVA                5                 4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  7Q GAIN MUTATED    4 17 52  9
  7Q GAIN WILD-TYPE  5 12 57  5
D14V4, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  T1               4                 5
  T2              17                12
  T3              52                57
  T4               9                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  7Q GAIN MUTATED   35 28 18
  7Q GAIN WILD-TYPE 48 17 14
D14V5, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  N0              35                48
  N1              28                17
  N2              18                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  7Q GAIN MUTATED   58 14   1  8
  7Q GAIN WILD-TYPE 65  8   1  5
D14V6, multiclass
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  M0               58                65
  M1               14                 8
  M1A               1                 1
  MX                8                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   36 47
  7Q GAIN WILD-TYPE 38 41
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     36   47
  7Q GAIN WILD-TYPE   38   41
        clus
vv       7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  FEMALE              36                38
  MALE                47                41
[1] 2 2
[1] FALSE
D14V8, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED   79  2
  7Q GAIN WILD-TYPE 64 11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED     79    2
  7Q GAIN WILD-TYPE   64   11
                                clus
vv                               7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       79                64
  RECTAL MUCINOUS ADENOCARCINOMA               2                11
[1] 2 2
[1] FALSE
D14V9, binary
                   cls
clus                 0  1
  7Q GAIN MUTATED    3 80
  7Q GAIN WILD-TYPE  3 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q GAIN MUTATED      3   80
  7Q GAIN WILD-TYPE    3   76
     clus
vv    7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  NO                3                 3
  YES              80                76
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  7Q GAIN MUTATED   61  1  8  3
  7Q GAIN WILD-TYPE 60  1  4  0
D14V10, multiclass
    clus
vv   7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  R0              61                60
  R1               1                 1
  R2               8                 4
  RX               3                 0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q GAIN MUTATED       1                         3    43
  7Q GAIN WILD-TYPE     0                         0    38
D14V12, multiclass
                           clus
vv                          7Q GAIN MUTATED 7Q GAIN WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               3                 0
  WHITE                                  43                38
[1] 3 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   31  5
  8P GAIN WILD-TYPE 97 17
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
               36               114 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
                5                17 
$`8P GAIN MUTATED`
TCGA-AF-3400 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3598 TCGA-AG-3731 
       12.72        20.02        36.03        32.02        50.04         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 
       36.95         1.02        48.03        32.02         1.02         0.99 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A032 TCGA-AH-6544 
        9.07        31.00        70.03        64.01        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-6156 
        0.69         0.72         6.05         9.37         7.99        15.02 
TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 
       13.05        41.36        57.24        24.13         0.49        17.00 
TCGA-EI-6514 TCGA-EI-6883 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 TCGA-G5-6572 
       16.31        11.51        37.51         0.39         0.76        47.08 

$`8P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 
       37.74        10.39        14.50         8.45        15.39        10.39 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 
       17.03        13.02        35.01        14.01        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01J 
       25.97        23.01        37.02        15.95        36.03         1.02 
TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       61.97        41.00         1.45         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 
        6.05         6.97         4.73        13.97        60.03        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        10.06         5.29       126.44 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
      129.27        51.48        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       20.91        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        14.86         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.12         0.46        18.28        55.76        26.43 

  8P GAIN MUTATED 8P GAIN WILD-TYPE 
             0.39              0.46 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
            70.03            129.27 
  8P GAIN MUTATED 8P GAIN WILD-TYPE 
           15.665            14.025 
[1] "0.4 - 70.0 (15.7)"  "0.5 - 129.3 (14.0)"
[1] "hr=" "1.4"
D15V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P GAIN MUTATED         2        4        13         1         1         1
  8P GAIN WILD-TYPE      28        4        25         1         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P GAIN MUTATED            1          3          3        6         1
  8P GAIN WILD-TYPE          8         20         11       12         8
D15V3, multiclass
            clus
vv           8P GAIN MUTATED 8P GAIN WILD-TYPE
  STAGE I                  2                28
  STAGE II                 4                 4
  STAGE IIA               13                25
  STAGE IIB                1                 1
  STAGE IIC                1                 1
  STAGE III                1                 4
  STAGE IIIA               1                 8
  STAGE IIIB               3                20
  STAGE IIIC               3                11
  STAGE IV                 6                12
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P GAIN MUTATED    1  3 30  4
  8P GAIN WILD-TYPE  8 26 79 10
D15V4, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              30                79
  T4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  8P GAIN MUTATED   22  8  7
  8P GAIN WILD-TYPE 61 37 25
D15V5, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  N0              22                61
  N1               8                37
  N2               7                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  8P GAIN MUTATED   27  7   1  3
  8P GAIN WILD-TYPE 96 15   1 10
D15V6, multiclass
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  M0               27                96
  M1                7                15
  M1A               1                 1
  MX                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                   cls
clus                 0  1
  8P GAIN MUTATED   16 23
  8P GAIN WILD-TYPE 58 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     16   23
  8P GAIN WILD-TYPE   58   65
        clus
vv       8P GAIN MUTATED 8P GAIN WILD-TYPE
  FEMALE              16                58
  MALE                23                65
[1] 2 2
[1] FALSE
D15V8, binary
                   cls
clus                  0   1
  8P GAIN MUTATED    35   3
  8P GAIN WILD-TYPE 108  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED     35    3
  8P GAIN WILD-TYPE  108   10
                                clus
vv                               8P GAIN MUTATED 8P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       35               108
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D15V9, binary
                   cls
clus                  0   1
  8P GAIN MUTATED     1  38
  8P GAIN WILD-TYPE   5 118
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P GAIN MUTATED      1   38
  8P GAIN WILD-TYPE    5  118
     clus
vv    8P GAIN MUTATED 8P GAIN WILD-TYPE
  NO                1                 5
  YES              38               118
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P GAIN MUTATED   23  0  5  1
  8P GAIN WILD-TYPE 98  2  7  2
D15V10, multiclass
    clus
vv   8P GAIN MUTATED 8P GAIN WILD-TYPE
  R0              23                98
  R1               0                 2
  R2               5                 7
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P GAIN MUTATED       0                         0    22
  8P GAIN WILD-TYPE     1                         3    59
D15V12, multiclass
                           clus
vv                          8P GAIN MUTATED 8P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                  22                59
[1] 3 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   64 17
  8Q GAIN WILD-TYPE 64  5
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               81                69 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
               17                 5 
$`8Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        12.72        37.74 
TCGA-AF-3913 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 
       10.39        20.02        10.39        36.03        32.02         1.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3612 
       24.00         1.02        46.03        50.04         6.05        19.99 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
        7.99         1.02        32.98        36.95        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
        0.99        25.97        37.02        15.95         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A032 
       31.00        70.03        64.01        51.98         1.94        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 
        0.49         1.45         0.69         0.72        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 
        9.37         4.73        60.03         7.99        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       15.02         7.10        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 
       57.24        24.13        32.61         0.49        17.00        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 
       16.31        11.51        10.78        13.64         9.96        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
       14.86         0.39         1.02         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

$`8Q GAIN WILD-TYPE`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 
       13.55        19.10        14.50         8.45        15.39        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
        8.02         7.07         2.01        34.03         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
        0.99        15.95        19.99         0.99        29.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99         1.02        13.02        35.01        14.01 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       19.99        36.03        20.98        13.94         6.02        23.01 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N 
       36.03        12.00        10.98        49.97        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
       41.00         4.60         1.81         6.05         6.97        13.97 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 
       10.98        11.01        15.02        12.00        36.00        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 
       12.95         5.29       129.27        51.48         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 
       19.96        20.91        18.28        15.85        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 
        8.61        17.46        11.97         8.45        31.30         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.69         0.53         1.12 

  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
             0.39              0.53 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
           126.44            129.27 
  8Q GAIN MUTATED 8Q GAIN WILD-TYPE 
            15.95             13.94 
[1] "0.4 - 126.4 (15.9)" "0.5 - 129.3 (13.9)"
[1] "hr=" "2.1"
D16V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q GAIN MUTATED        10        5        22         1         2         2
  8Q GAIN WILD-TYPE      20        3        16         1         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q GAIN MUTATED            5         10         11       14         2
  8Q GAIN WILD-TYPE          4         13          3        4         7
D16V3, multiclass
            clus
vv           8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  STAGE I                 10                20
  STAGE II                 5                 3
  STAGE IIA               22                16
  STAGE IIB                1                 1
  STAGE IIC                2                 0
  STAGE III                2                 3
  STAGE IIIA               5                 4
  STAGE IIIB              10                13
  STAGE IIIC              11                 3
  STAGE IV                14                 4
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8Q GAIN MUTATED    3 12 63  9
  8Q GAIN WILD-TYPE  6 17 46  5
D16V4, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  T1               3                 6
  T2              12                17
  T3              63                46
  T4               9                 5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  8Q GAIN MUTATED   41 23 22
  8Q GAIN WILD-TYPE 42 22 10
D16V5, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  N0              41                42
  N1              23                22
  N2              22                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  8Q GAIN MUTATED   61 15   1  9
  8Q GAIN WILD-TYPE 62  7   1  4
D16V6, multiclass
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  M0               61                62
  M1               15                 7
  M1A               1                 1
  MX                9                 4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   39 49
  8Q GAIN WILD-TYPE 35 39
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     39   49
  8Q GAIN WILD-TYPE   35   39
        clus
vv       8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  FEMALE              39                35
  MALE                49                39
[1] 2 2
[1] FALSE
D16V8, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED   82  4
  8Q GAIN WILD-TYPE 61  9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED     82    4
  8Q GAIN WILD-TYPE   61    9
                                clus
vv                               8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       82                61
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
D16V9, binary
                   cls
clus                 0  1
  8Q GAIN MUTATED    5 83
  8Q GAIN WILD-TYPE  1 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q GAIN MUTATED      5   83
  8Q GAIN WILD-TYPE    1   73
     clus
vv    8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  NO                5                 1
  YES              83                73
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8Q GAIN MUTATED   58  2  9  2
  8Q GAIN WILD-TYPE 63  0  3  1
D16V10, multiclass
    clus
vv   8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  R0              58                63
  R1               2                 0
  R2               9                 3
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q GAIN MUTATED       0                         2    47
  8Q GAIN WILD-TYPE     1                         1    34
D16V12, multiclass
                           clus
vv                          8Q GAIN MUTATED 8Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  47                34
[1] 3 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   29  8
  9P GAIN WILD-TYPE 99 14
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
               37               113 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
                8                14 
$`9P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3587 
       17.95        17.23        12.72        10.39        20.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3878 
        2.01        50.04         0.99        19.99         7.99         0.99 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-A01W TCGA-AG-A020 
       17.03         1.02        32.02        36.03        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 
       51.98        38.04         0.69         0.72        10.98        36.00 
TCGA-DY-A1DE TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6464 
      129.27         2.40        11.51        10.78         8.45         9.96 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
       14.86         0.39         0.69         1.12         0.46        18.28 
TCGA-G5-6641 
       26.43 

$`9P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       24.13        43.04        13.55        19.10        37.74        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
        8.45        15.39        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3727 
       34.03        12.03         6.05        15.95        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 
       36.95        13.02        35.01        14.01        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        31.00        64.01 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        1.45         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       13.64        17.46        11.97        37.51        31.30         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.53         0.76        55.76        47.08 

  9P GAIN MUTATED 9P GAIN WILD-TYPE 
             0.39              0.49 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
           129.27            126.44 
  9P GAIN MUTATED 9P GAIN WILD-TYPE 
            11.51             15.02 
[1] "0.4 - 129.3 (11.5)" "0.5 - 126.4 (15.0)"
[1] "hr=" "1.7"
D17V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P GAIN MUTATED         6        1        12         0         2         2
  9P GAIN WILD-TYPE      24        7        26         2         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P GAIN MUTATED            4          3          5        4         2
  9P GAIN WILD-TYPE          5         20          9       14         7
D17V3, multiclass
            clus
vv           9P GAIN MUTATED 9P GAIN WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA               12                26
  STAGE IIB                0                 2
  STAGE IIC                2                 0
  STAGE III                2                 3
  STAGE IIIA               4                 5
  STAGE IIIB               3                20
  STAGE IIIC               5                 9
  STAGE IV                 4                14
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P GAIN MUTATED    1  7 30  4
  9P GAIN WILD-TYPE  8 22 79 10
D17V4, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  T1               1                 8
  T2               7                22
  T3              30                79
  T4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9P GAIN MUTATED   21 10 10
  9P GAIN WILD-TYPE 62 35 22
D17V5, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  N0              21                62
  N1              10                35
  N2              10                22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  9P GAIN MUTATED   35  5   0  2
  9P GAIN WILD-TYPE 88 17   2 11
D17V6, multiclass
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  M0               35                88
  M1                5                17
  M1A               0                 2
  MX                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                   cls
clus                 0  1
  9P GAIN MUTATED   19 23
  9P GAIN WILD-TYPE 55 65
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     19   23
  9P GAIN WILD-TYPE   55   65
        clus
vv       9P GAIN MUTATED 9P GAIN WILD-TYPE
  FEMALE              19                55
  MALE                23                65
[1] 2 2
[1] FALSE
D17V8, binary
                   cls
clus                  0   1
  9P GAIN MUTATED    36   5
  9P GAIN WILD-TYPE 107   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED     36    5
  9P GAIN WILD-TYPE  107    8
                                clus
vv                               9P GAIN MUTATED 9P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       36               107
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 2 2
[1] FALSE
D17V9, binary
                   cls
clus                  0   1
  9P GAIN MUTATED     1  41
  9P GAIN WILD-TYPE   5 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P GAIN MUTATED      1   41
  9P GAIN WILD-TYPE    5  115
     clus
vv    9P GAIN MUTATED 9P GAIN WILD-TYPE
  NO                1                 5
  YES              41               115
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9P GAIN MUTATED   37  0  2  0
  9P GAIN WILD-TYPE 84  2 10  3
D17V10, multiclass
    clus
vv   9P GAIN MUTATED 9P GAIN WILD-TYPE
  R0              37                84
  R1               0                 2
  R2               2                10
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P GAIN MUTATED       0                         2    20
  9P GAIN WILD-TYPE     1                         1    61
D17V12, multiclass
                           clus
vv                          9P GAIN MUTATED 9P GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  20                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(18) Variable = 9Q GAIN MUTATION ANALYSIS
D18V1, survival
                   sevent
clus2                 0   1
  9Q GAIN MUTATED    22   6
  9Q GAIN WILD-TYPE 106  16
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
               28               122 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
                6                16 
$`9Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3594 TCGA-AG-3598 
       17.95        12.72        10.39        20.02         2.01        50.04 
TCGA-AG-3605 TCGA-AG-3878 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-A020 
        0.99         0.99        17.03         1.02        32.02        10.98 
TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6644 TCGA-DC-4745 TCGA-DC-6157 TCGA-DY-A1DE 
       51.98        38.04         0.72        10.98        36.00       129.27 
TCGA-EF-5831 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 
        2.40        11.51        10.78         9.96         0.39         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        1.12         0.46        18.28        26.43 

$`9Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
        1.02        46.03        34.03        12.03         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       35.01        14.01        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       49.97         1.94        38.96        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
        8.61        13.64        17.46        11.97         8.45        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
       31.30        14.86         1.02         0.66         0.53         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
             0.39              0.49 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
           129.27            126.44 
  9Q GAIN MUTATED 9Q GAIN WILD-TYPE 
            10.98             15.02 
[1] "0.4 - 129.3 (11.0)" "0.5 - 126.4 (15.0)"
[1] "hr=" "1.9"
D18V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q GAIN MUTATED         4        0        11         0         2         2
  9Q GAIN WILD-TYPE      26        8        27         2         0         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q GAIN MUTATED            4          2          3        4         0
  9Q GAIN WILD-TYPE          5         21         11       14         9
D18V3, multiclass
            clus
vv           9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  STAGE I                  4                26
  STAGE II                 0                 8
  STAGE IIA               11                27
  STAGE IIB                0                 2
  STAGE IIC                2                 0
  STAGE III                2                 3
  STAGE IIIA               4                 5
  STAGE IIIB               2                21
  STAGE IIIC               3                11
  STAGE IV                 4                14
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q GAIN MUTATED    1  5 24  3
  9Q GAIN WILD-TYPE  8 24 85 11
D18V4, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  T1               1                 8
  T2               5                24
  T3              24                85
  T4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9Q GAIN MUTATED   17  8  7
  9Q GAIN WILD-TYPE 66 37 25
D18V5, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  N0              17                66
  N1               8                37
  N2               7                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  9Q GAIN MUTATED   27  4   0  2
  9Q GAIN WILD-TYPE 96 18   2 11
D18V6, multiclass
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  M0               27                96
  M1                4                18
  M1A               0                 2
  MX                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                   cls
clus                 0  1
  9Q GAIN MUTATED   13 20
  9Q GAIN WILD-TYPE 61 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     13   20
  9Q GAIN WILD-TYPE   61   68
        clus
vv       9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  FEMALE              13                61
  MALE                20                68
[1] 2 2
[1] FALSE
D18V8, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED    28   4
  9Q GAIN WILD-TYPE 115   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED     28    4
  9Q GAIN WILD-TYPE  115    9
                                clus
vv                               9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       28               115
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
D18V9, binary
                   cls
clus                  0   1
  9Q GAIN MUTATED     1  32
  9Q GAIN WILD-TYPE   5 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q GAIN MUTATED      1   32
  9Q GAIN WILD-TYPE    5  124
     clus
vv    9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  NO                1                 5
  YES              32               124
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  9Q GAIN MUTATED   28  0  2  0
  9Q GAIN WILD-TYPE 93  2 10  3
D18V10, multiclass
    clus
vv   9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  R0              28                93
  R1               0                 2
  R2               2                10
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q GAIN MUTATED       0                         2    16
  9Q GAIN WILD-TYPE     1                         1    65
D18V12, multiclass
                           clus
vv                          9Q GAIN MUTATED 9Q GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  16                65
[1] 3 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     9   2
  10P GAIN WILD-TYPE 119  20
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                11                139 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
                 2                 20 
$`10P GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-3728 TCGA-AG-3902 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01W 
       17.95        29.98        32.02        15.95         9.07        70.03 
TCGA-BM-6198 TCGA-DC-4745 TCGA-DY-A1DF TCGA-F5-6571 TCGA-F5-6812 
       10.19        10.98        24.13        31.30         0.66 

$`10P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        19.99         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
       36.03         1.02        12.00        31.00        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       13.97        60.03         7.99        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       37.51        14.86         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  10P GAIN MUTATED 10P GAIN WILD-TYPE 
              0.66               0.39 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             70.03             129.27 
  10P GAIN MUTATED 10P GAIN WILD-TYPE 
             17.95              14.01 
[1] "0.7 - 70.0 (17.9)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.1"
D19V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P GAIN MUTATED         1        1         4         0         0         0
  10P GAIN WILD-TYPE      29        7        34         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P GAIN MUTATED            0          3          1        2         0
  10P GAIN WILD-TYPE          9         20         13       16         9
D19V3, multiclass
            clus
vv           10P GAIN MUTATED 10P GAIN WILD-TYPE
  STAGE I                   1                 29
  STAGE II                  1                  7
  STAGE IIA                 4                 34
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                3                 20
  STAGE IIIC                1                 13
  STAGE IV                  2                 16
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P GAIN MUTATED    0  1 11  0
  10P GAIN WILD-TYPE  9 28 98 14
D19V4, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3               11                 98
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10P GAIN MUTATED    6  3  3
  10P GAIN WILD-TYPE 77 42 29
D19V5, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  N0                6                 77
  N1                3                 42
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  10P GAIN MUTATED     9   2   0   0
  10P GAIN WILD-TYPE 114  20   2  13
D19V6, multiclass
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  M0                 9                114
  M1                 2                 20
  M1A                0                  2
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                    cls
clus                  0  1
  10P GAIN MUTATED    6  6
  10P GAIN WILD-TYPE 68 82
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      6    6
  10P GAIN WILD-TYPE   68   82
        clus
vv       10P GAIN MUTATED 10P GAIN WILD-TYPE
  FEMALE                6                 68
  MALE                  6                 82
[1] 2 2
[1] FALSE
D19V8, binary
                    cls
clus                   0   1
  10P GAIN MUTATED    12   0
  10P GAIN WILD-TYPE 131  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED     12    0
  10P GAIN WILD-TYPE  131   13
                                clus
vv                               10P GAIN MUTATED 10P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        12                131
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D19V9, binary
                    cls
clus                   0   1
  10P GAIN MUTATED     1  11
  10P GAIN WILD-TYPE   5 145
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P GAIN MUTATED      1   11
  10P GAIN WILD-TYPE    5  145
     clus
vv    10P GAIN MUTATED 10P GAIN WILD-TYPE
  NO                 1                  5
  YES               11                145
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10P GAIN MUTATED    10   0   1   0
  10P GAIN WILD-TYPE 111   2  11   3
D19V10, multiclass
    clus
vv   10P GAIN MUTATED 10P GAIN WILD-TYPE
  R0               10                111
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P GAIN MUTATED       0                         0     6
  10P GAIN WILD-TYPE     1                         3    75
D19V12, multiclass
                           clus
vv                          10P GAIN MUTATED 10P GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    6                 75
[1] 3 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   1
  10Q GAIN WILD-TYPE 124  21
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 5                145 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
                 1                 21 
$`10Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-3999 TCGA-AG-A01W TCGA-BM-6198 TCGA-DC-4745 
       17.95        28.04        70.03        10.19        10.98 

$`10Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60         1.81         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             10.19               0.39 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             70.03             129.27 
  10Q GAIN MUTATED 10Q GAIN WILD-TYPE 
             17.95              14.04 
[1] "10.2 - 70.0 (17.9)" "0.4 - 129.3 (14.0)"
[1] "hr=" "1.2"
D20V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q GAIN MUTATED         0        1         1         0         0         0
  10Q GAIN WILD-TYPE      30        7        37         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q GAIN MUTATED            0          2          1        1         0
  10Q GAIN WILD-TYPE          9         21         13       17         9
D20V3, multiclass
            clus
vv           10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  1                  7
  STAGE IIA                 1                 37
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                2                 21
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  10Q GAIN MUTATED     0   0   6   0
  10Q GAIN WILD-TYPE   9  29 103  14
D20V4, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  T1                0                  9
  T2                0                 29
  T3                6                103
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10Q GAIN MUTATED    2  2  2
  10Q GAIN WILD-TYPE 81 43 30
D20V5, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  N0                2                 81
  N1                2                 43
  N2                2                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  10Q GAIN MUTATED     4   1   0   0
  10Q GAIN WILD-TYPE 119  21   2  13
D20V6, multiclass
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  M0                 4                119
  M1                 1                 21
  M1A                0                  2
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                    cls
clus                  0  1
  10Q GAIN MUTATED    5  1
  10Q GAIN WILD-TYPE 69 87
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      5    1
  10Q GAIN WILD-TYPE   69   87
        clus
vv       10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  1                 87
[1] 2 2
[1] FALSE
D20V8, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     6   0
  10Q GAIN WILD-TYPE 137  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      6    0
  10Q GAIN WILD-TYPE  137   13
                                clus
vv                               10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D20V9, binary
                    cls
clus                   0   1
  10Q GAIN MUTATED     1   5
  10Q GAIN WILD-TYPE   5 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q GAIN MUTATED      1    5
  10Q GAIN WILD-TYPE    5  151
     clus
vv    10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  NO                 1                  5
  YES                5                151
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  10Q GAIN MUTATED     6   0   0   0
  10Q GAIN WILD-TYPE 115   2  12   3
D20V10, multiclass
    clus
vv   10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  R0                6                115
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q GAIN MUTATED       0                         0     3
  10Q GAIN WILD-TYPE     1                         3    78
D20V12, multiclass
                           clus
vv                          10Q GAIN MUTATED 10Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    3                 78
[1] 3 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    24   3
  11P GAIN WILD-TYPE 104  19
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                27                123 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
                 3                 19 
$`11P GAIN MUTATED`
TCGA-AF-2690 TCGA-AF-3913 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3609 
       17.23        10.39        20.02        12.00        46.03        19.99 
TCGA-AG-3612 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 
       19.99        36.03         1.02        25.97        31.00         4.60 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       10.19         9.37         4.73        11.01        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6514 TCGA-EI-6885 
       36.00        30.05       126.44         2.40        16.31        13.64 
TCGA-F5-6810 TCGA-F5-6811 TCGA-G5-6233 
        0.39         1.02        18.28 

$`11P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 
       37.74        14.50         8.45        15.39        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 
       32.02        19.99        28.04        14.04        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        1.81         6.05         6.05         6.97        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        10.98        15.02        13.97        15.02         7.10 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
      129.27        24.13        51.48        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.34        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  11P GAIN MUTATED 11P GAIN WILD-TYPE 
              0.39               0.46 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
            126.44             129.27 
  11P GAIN MUTATED 11P GAIN WILD-TYPE 
             13.64              14.50 
[1] "0.4 - 126.4 (13.6)" "0.5 - 129.3 (14.5)"
[1] "hr=" "1.2"
D21V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P GAIN MUTATED         7        1        10         0         1         0
  11P GAIN WILD-TYPE      23        7        28         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P GAIN MUTATED            1          3          2        4         1
  11P GAIN WILD-TYPE          8         20         12       14         8
D21V3, multiclass
            clus
vv           11P GAIN MUTATED 11P GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  1                  7
  STAGE IIA                10                 28
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 0                  5
  STAGE IIIA                1                  8
  STAGE IIIB                3                 20
  STAGE IIIC                2                 12
  STAGE IV                  4                 14
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P GAIN MUTATED    1  8 19  2
  11P GAIN WILD-TYPE  8 21 90 12
D21V4, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  T1                1                  8
  T2                8                 21
  T3               19                 90
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11P GAIN MUTATED   19  6  5
  11P GAIN WILD-TYPE 64 39 27
D21V5, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  N0               19                 64
  N1                6                 39
  N2                5                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  11P GAIN MUTATED   24  5   0  0
  11P GAIN WILD-TYPE 99 17   2 13
D21V6, multiclass
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  M0                24                 99
  M1                 5                 17
  M1A                0                  2
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                    cls
clus                  0  1
  11P GAIN MUTATED   13 17
  11P GAIN WILD-TYPE 61 71
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     13   17
  11P GAIN WILD-TYPE   61   71
        clus
vv       11P GAIN MUTATED 11P GAIN WILD-TYPE
  FEMALE               13                 61
  MALE                 17                 71
[1] 2 2
[1] FALSE
D21V8, binary
                    cls
clus                   0   1
  11P GAIN MUTATED    30   0
  11P GAIN WILD-TYPE 113  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED     30    0
  11P GAIN WILD-TYPE  113   13
                                clus
vv                               11P GAIN MUTATED 11P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D21V9, binary
                    cls
clus                   0   1
  11P GAIN MUTATED     1  29
  11P GAIN WILD-TYPE   5 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P GAIN MUTATED      1   29
  11P GAIN WILD-TYPE    5  127
     clus
vv    11P GAIN MUTATED 11P GAIN WILD-TYPE
  NO                 1                  5
  YES               29                127
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11P GAIN MUTATED   24  0  2  0
  11P GAIN WILD-TYPE 97  2 10  3
D21V10, multiclass
    clus
vv   11P GAIN MUTATED 11P GAIN WILD-TYPE
  R0               24                 97
  R1                0                  2
  R2                2                 10
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P GAIN MUTATED       0                         3    16
  11P GAIN WILD-TYPE     1                         0    65
D21V12, multiclass
                           clus
vv                          11P GAIN MUTATED 11P GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   16                 65
[1] 3 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    22   2
  11Q GAIN WILD-TYPE 106  20
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                24                126 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
                 2                 20 
$`11Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3612 TCGA-AG-3883 
       17.23        10.39        12.00        46.03        19.99         1.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-CI-6623 
       36.03         1.02        25.97        31.00         4.60         9.37 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        4.73        11.01        12.99        12.00        15.02        36.00 
TCGA-DY-A0XA TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
      126.44        16.31        13.64         0.39         1.02         0.66 

$`11Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        14.04        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         1.81        10.19         6.05         6.05         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
       13.97        60.03         7.99        10.98        15.02        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       37.51        31.30        14.86         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
              0.39               0.46 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            126.44             129.27 
  11Q GAIN MUTATED 11Q GAIN WILD-TYPE 
            12.495             14.940 
[1] "0.4 - 126.4 (12.5)" "0.5 - 129.3 (14.9)"
[1] "hr=" "1.5"
D22V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q GAIN MUTATED         7        1         8         0         0         0
  11Q GAIN WILD-TYPE      23        7        30         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q GAIN MUTATED            0          2          1        4         2
  11Q GAIN WILD-TYPE          9         21         13       14         7
D22V3, multiclass
            clus
vv           11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  1                  7
  STAGE IIA                 8                 30
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                2                 21
  STAGE IIIC                1                 13
  STAGE IV                  4                 14
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q GAIN MUTATED    1  7 14  3
  11Q GAIN WILD-TYPE  8 22 95 11
D22V4, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 22
  T3               14                 95
  T4                3                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11Q GAIN MUTATED   17  4  4
  11Q GAIN WILD-TYPE 66 41 28
D22V5, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  N0               17                 66
  N1                4                 41
  N2                4                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  11Q GAIN MUTATED    19   5   1   0
  11Q GAIN WILD-TYPE 104  17   1  13
D22V6, multiclass
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  M0                19                104
  M1                 5                 17
  M1A                1                  1
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                    cls
clus                  0  1
  11Q GAIN MUTATED   11 14
  11Q GAIN WILD-TYPE 63 74
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     11   14
  11Q GAIN WILD-TYPE   63   74
        clus
vv       11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  FEMALE               11                 63
  MALE                 14                 74
[1] 2 2
[1] FALSE
D22V8, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED    25   0
  11Q GAIN WILD-TYPE 118  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED     25    0
  11Q GAIN WILD-TYPE  118   13
                                clus
vv                               11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        25                118
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D22V9, binary
                    cls
clus                   0   1
  11Q GAIN MUTATED     0  25
  11Q GAIN WILD-TYPE   6 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q GAIN MUTATED      0   25
  11Q GAIN WILD-TYPE    6  131
     clus
vv    11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  NO                 0                  6
  YES               25                131
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11Q GAIN MUTATED    19   0   2   0
  11Q GAIN WILD-TYPE 102   2  10   3
D22V10, multiclass
    clus
vv   11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  R0               19                102
  R1                0                  2
  R2                2                 10
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q GAIN MUTATED       0                         3    13
  11Q GAIN WILD-TYPE     1                         0    68
D22V12, multiclass
                           clus
vv                          11Q GAIN MUTATED 11Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   13                 68
[1] 3 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    24   6
  12P GAIN WILD-TYPE 104  16
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                30                120 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
                 6                 16 
$`12P GAIN MUTATED`
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3587 
       12.72        37.74         8.45        10.39        36.03        46.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3883 TCGA-AG-3887 
        2.01         6.05        19.99         7.99         1.02        36.95 
TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N 
        1.02        36.03        15.95        36.03        38.96        61.97 
TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 
       60.03        13.05        10.06         5.29       126.44        32.61 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 
       19.96        18.28        17.69        13.64        11.97        18.28 

$`12P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 
       10.39        14.50        15.39        20.02        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       34.03        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       19.99        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       37.02         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X 
       64.01        10.98        51.98        49.97         1.94        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       30.05        12.95        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76         0.46        55.76        47.08        26.43 

  12P GAIN MUTATED 12P GAIN WILD-TYPE 
              1.02               0.39 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            126.44             129.27 
  12P GAIN MUTATED 12P GAIN WILD-TYPE 
            17.985             13.990 
[1] "1.0 - 126.4 (18.0)" "0.4 - 129.3 (14.0)"
[1] "hr=" "1"  
D23V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P GAIN MUTATED         7        3         9         0         1         0
  12P GAIN WILD-TYPE      23        5        29         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P GAIN MUTATED            1          3          4        4         1
  12P GAIN WILD-TYPE          8         20         10       14         8
D23V3, multiclass
            clus
vv           12P GAIN MUTATED 12P GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  3                  5
  STAGE IIA                 9                 29
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 0                  5
  STAGE IIIA                1                  8
  STAGE IIIB                3                 20
  STAGE IIIC                4                 10
  STAGE IV                  4                 14
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P GAIN MUTATED    1  9 21  2
  12P GAIN WILD-TYPE  8 20 88 12
D23V4, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  T1                1                  8
  T2                9                 20
  T3               21                 88
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12P GAIN MUTATED   20  6  7
  12P GAIN WILD-TYPE 63 39 25
D23V5, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  N0               20                 63
  N1                6                 39
  N2                7                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  12P GAIN MUTATED   26  3   0  4
  12P GAIN WILD-TYPE 97 19   2  9
D23V6, multiclass
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  M0                26                 97
  M1                 3                 19
  M1A                0                  2
  MX                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                    cls
clus                  0  1
  12P GAIN MUTATED   14 19
  12P GAIN WILD-TYPE 60 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     14   19
  12P GAIN WILD-TYPE   60   69
        clus
vv       12P GAIN MUTATED 12P GAIN WILD-TYPE
  FEMALE               14                 60
  MALE                 19                 69
[1] 2 2
[1] FALSE
D23V8, binary
                    cls
clus                   0   1
  12P GAIN MUTATED    28   4
  12P GAIN WILD-TYPE 115   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED     28    4
  12P GAIN WILD-TYPE  115    9
                                clus
vv                               12P GAIN MUTATED 12P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        28                115
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
D23V9, binary
                    cls
clus                   0   1
  12P GAIN MUTATED     3  30
  12P GAIN WILD-TYPE   3 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P GAIN MUTATED      3   30
  12P GAIN WILD-TYPE    3  126
     clus
vv    12P GAIN MUTATED 12P GAIN WILD-TYPE
  NO                 3                  3
  YES               30                126
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  12P GAIN MUTATED   24  0  2  2
  12P GAIN WILD-TYPE 97  2 10  1
D23V10, multiclass
    clus
vv   12P GAIN MUTATED 12P GAIN WILD-TYPE
  R0               24                 97
  R1                0                  2
  R2                2                 10
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P GAIN MUTATED       1                         0    15
  12P GAIN WILD-TYPE     0                         3    66
D23V12, multiclass
                           clus
vv                          12P GAIN MUTATED 12P GAIN WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   15                 66
[1] 3 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    14   6
  12Q GAIN WILD-TYPE 114  16
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                20                130 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
                 6                 16 
$`12Q GAIN MUTATED`
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3594 TCGA-AG-3609 TCGA-AG-3883 
       12.72         8.45        36.03         2.01        19.99         1.02 
TCGA-AG-3896 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-DC-6682 TCGA-DC-6683 
        1.02        36.03        38.96        61.97        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
      126.44        32.61        19.96        18.28        17.69        13.64 
TCGA-EI-7002 TCGA-G5-6233 
       11.97        18.28 

$`12Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        15.95         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        36.00         7.10        30.05        12.95         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
        2.40        20.55        20.91        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
              1.02               0.39 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            126.44             129.27 
  12Q GAIN MUTATED 12Q GAIN WILD-TYPE 
            17.985             14.025 
[1] "1.0 - 126.4 (18.0)" "0.4 - 129.3 (14.0)"
[1] "hr=" "1.9"
D24V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q GAIN MUTATED         4        2         7         0         1         0
  12Q GAIN WILD-TYPE      26        6        31         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q GAIN MUTATED            1          3          1        3         1
  12Q GAIN WILD-TYPE          8         20         13       15         8
D24V3, multiclass
            clus
vv           12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  STAGE I                   4                 26
  STAGE II                  2                  6
  STAGE IIA                 7                 31
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 0                  5
  STAGE IIIA                1                  8
  STAGE IIIB                3                 20
  STAGE IIIC                1                 13
  STAGE IV                  3                 15
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q GAIN MUTATED    1  6 15  1
  12Q GAIN WILD-TYPE  8 23 94 13
D24V4, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               15                 94
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12Q GAIN MUTATED   14  6  3
  12Q GAIN WILD-TYPE 69 39 29
D24V5, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  N0               14                 69
  N1                6                 39
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12Q GAIN MUTATED    19   3   0   1
  12Q GAIN WILD-TYPE 104  19   2  12
D24V6, multiclass
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  M0                19                104
  M1                 3                 19
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                    cls
clus                  0  1
  12Q GAIN MUTATED   12 11
  12Q GAIN WILD-TYPE 62 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     12   11
  12Q GAIN WILD-TYPE   62   77
        clus
vv       12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  FEMALE               12                 62
  MALE                 11                 77
[1] 2 2
[1] FALSE
D24V8, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED    20   2
  12Q GAIN WILD-TYPE 123  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED     20    2
  12Q GAIN WILD-TYPE  123   11
                                clus
vv                               12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
D24V9, binary
                    cls
clus                   0   1
  12Q GAIN MUTATED     1  22
  12Q GAIN WILD-TYPE   5 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q GAIN MUTATED      1   22
  12Q GAIN WILD-TYPE    5  134
     clus
vv    12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  NO                 1                  5
  YES               22                134
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q GAIN MUTATED    18   0   2   0
  12Q GAIN WILD-TYPE 103   2  10   3
D24V10, multiclass
    clus
vv   12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                2                 10
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q GAIN MUTATED       0                         0    12
  12Q GAIN WILD-TYPE     1                         3    69
D24V12, multiclass
                           clus
vv                          12Q GAIN MUTATED 12Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   12                 69
[1] 3 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   85 18
  13Q GAIN WILD-TYPE 43  4
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
               103                 47 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
                18                  4 
$`13Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         1.02         2.01         1.02        46.03        34.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
        0.99        19.99        19.99         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       19.99        36.95        17.03        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 
       17.03         0.99         6.02        25.97        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        9.07        12.00        70.03        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.96        38.04         0.49         0.69         0.72 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        4.60         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       12.00        36.00         7.10        30.05        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        0.49        20.55        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 
       16.34        16.31        16.41        11.51        10.78        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.66         0.69         0.76        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`13Q GAIN WILD-TYPE`
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72         8.45        36.03        12.00        32.02         8.02 
TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       24.00         2.01        50.04        12.03         6.05        15.95 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3892 
        7.99         1.02        32.98         0.99         1.02        13.02 
TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       48.03        20.98        13.94        23.01        37.02         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
       31.00        10.98        61.97        41.00         1.45         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6681 TCGA-DT-5265 
       10.19         6.05        13.97        15.02        12.95         5.29 
TCGA-DY-A0XA TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 
      126.44         2.40        19.96        20.91         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       17.46         8.45         0.53         1.12         0.46 

  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
              0.39               0.46 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
            129.27             126.44 
  13Q GAIN MUTATED 13Q GAIN WILD-TYPE 
             15.95              12.72 
[1] "0.4 - 129.3 (15.9)" "0.5 - 126.4 (12.7)"
[1] "hr=" "1.7"
D25V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q GAIN MUTATED        19        4        21         2         2         4
  13Q GAIN WILD-TYPE      11        4        17         0         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q GAIN MUTATED            6         19         12       13         5
  13Q GAIN WILD-TYPE          3          4          2        5         4
D25V3, multiclass
            clus
vv           13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  STAGE I                  19                 11
  STAGE II                  4                  4
  STAGE IIA                21                 17
  STAGE IIB                 2                  0
  STAGE IIC                 2                  0
  STAGE III                 4                  1
  STAGE IIIA                6                  3
  STAGE IIIB               19                  4
  STAGE IIIC               12                  2
  STAGE IV                 13                  5
  STAGE IVA                 5                  4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  13Q GAIN MUTATED    7 17 73 12
  13Q GAIN WILD-TYPE  2 12 36  2
D25V4, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  T1                7                  2
  T2               17                 12
  T3               73                 36
  T4               12                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  13Q GAIN MUTATED   48 35 25
  13Q GAIN WILD-TYPE 35 10  7
D25V5, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  N0               48                 35
  N1               35                 10
  N2               25                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  13Q GAIN MUTATED   81 16   0 12
  13Q GAIN WILD-TYPE 42  6   2  1
D25V6, multiclass
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  M0                81                 42
  M1                16                  6
  M1A                0                  2
  MX                12                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                    cls
clus                  0  1
  13Q GAIN MUTATED   48 62
  13Q GAIN WILD-TYPE 26 26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED     48   62
  13Q GAIN WILD-TYPE   26   26
        clus
vv       13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  FEMALE               48                 26
  MALE                 62                 26
[1] 2 2
[1] FALSE
D25V8, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED   103   3
  13Q GAIN WILD-TYPE  40  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED    103    3
  13Q GAIN WILD-TYPE   40   10
                                clus
vv                               13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       103                 40
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 2 2
[1] FALSE
D25V9, binary
                    cls
clus                   0   1
  13Q GAIN MUTATED     4 106
  13Q GAIN WILD-TYPE   2  50
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q GAIN MUTATED      4  106
  13Q GAIN WILD-TYPE    2   50
     clus
vv    13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  NO                 4                  2
  YES              106                 50
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  13Q GAIN MUTATED   78  2  8  2
  13Q GAIN WILD-TYPE 43  0  4  1
D25V10, multiclass
    clus
vv   13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  R0               78                 43
  R1                2                  0
  R2                8                  4
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q GAIN MUTATED       0                         3    61
  13Q GAIN WILD-TYPE     1                         0    20
D25V12, multiclass
                           clus
vv                          13Q GAIN MUTATED 13Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   61                 20
[1] 3 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     7   0
  14Q GAIN WILD-TYPE 121  22
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 7                143 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
                 0                 22 
$`14Q GAIN MUTATED`
TCGA-AF-6136 TCGA-AG-3999 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01Y TCGA-EI-6512 
       15.39        28.04        15.95        12.00        64.01        17.69 
TCGA-EI-6885 
       13.64 

$`14Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        37.74        10.39        14.50         8.45        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        36.03         9.07         1.02        31.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       20.91        17.00        18.28        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             12.00               0.39 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             64.01             129.27 
  14Q GAIN MUTATED 14Q GAIN WILD-TYPE 
             15.95              14.01 
[1] "12.0 - 64.0 (15.9)" "0.4 - 129.3 (14.0)"
[1] "hr="     "7.4e+07"
D26V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q GAIN MUTATED         1        1         1         0         0         0
  14Q GAIN WILD-TYPE      29        7        37         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q GAIN MUTATED            0          3          1        1         0
  14Q GAIN WILD-TYPE          9         20         13       17         9
D26V3, multiclass
            clus
vv           14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  STAGE I                   1                 29
  STAGE II                  1                  7
  STAGE IIA                 1                 37
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                3                 20
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  14Q GAIN MUTATED     0   1   7   0
  14Q GAIN WILD-TYPE   9  28 102  14
D26V4, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                7                102
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  14Q GAIN MUTATED    3  4  1
  14Q GAIN WILD-TYPE 80 41 31
D26V5, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  N0                3                 80
  N1                4                 41
  N2                1                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  14Q GAIN MUTATED     6   1   0   1
  14Q GAIN WILD-TYPE 117  21   2  12
D26V6, multiclass
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                    cls
clus                  0  1
  14Q GAIN MUTATED    5  3
  14Q GAIN WILD-TYPE 69 85
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      5    3
  14Q GAIN WILD-TYPE   69   85
        clus
vv       14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  3                 85
[1] 2 2
[1] FALSE
D26V8, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     8   0
  14Q GAIN WILD-TYPE 135  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      8    0
  14Q GAIN WILD-TYPE  135   13
                                clus
vv                               14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         8                135
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D26V9, binary
                    cls
clus                   0   1
  14Q GAIN MUTATED     1   7
  14Q GAIN WILD-TYPE   5 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q GAIN MUTATED      1    7
  14Q GAIN WILD-TYPE    5  149
     clus
vv    14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  NO                 1                  5
  YES                7                149
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  14Q GAIN MUTATED     7   0   0   0
  14Q GAIN WILD-TYPE 114   2  12   3
D26V10, multiclass
    clus
vv   14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q GAIN MUTATED       0                         0     3
  14Q GAIN WILD-TYPE     1                         3    78
D26V12, multiclass
                           clus
vv                          14Q GAIN MUTATED 14Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    3                 78
[1] 3 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     2   1
  15Q GAIN WILD-TYPE 126  21
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 3                147 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 1                 21 
$`15Q GAIN MUTATED`
TCGA-AG-A01W TCGA-EI-7004 TCGA-F5-6464 
       70.03         8.45         9.96 

$`15Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              8.45               0.39 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
             70.03             129.27 
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
              9.96              14.50 
[1] "8.4 - 70.0 (10.0)"  "0.4 - 129.3 (14.5)"
[1] "hr=" "1.1"
D27V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q GAIN MUTATED         0        1         0         0         0         0
  15Q GAIN WILD-TYPE      30        7        38         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q GAIN MUTATED            0          0          1        0         1
  15Q GAIN WILD-TYPE          9         23         13       18         8
D27V3, multiclass
            clus
vv           15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  1                  7
  STAGE IIA                 0                 38
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                0                 23
  STAGE IIIC                1                 13
  STAGE IV                  0                 18
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  15Q GAIN MUTATED     0   0   1   2
  15Q GAIN WILD-TYPE   9  29 108  12
D27V4, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  T1                0                  9
  T2                0                 29
  T3                1                108
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  15Q GAIN MUTATED    1  0  2
  15Q GAIN WILD-TYPE 82 45 30
D27V5, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  N0                1                 82
  N1                0                 45
  N2                2                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  15Q GAIN MUTATED     3   0   0   0
  15Q GAIN WILD-TYPE 120  22   2  13
D27V6, multiclass
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  M0                 3                120
  M1                 0                 22
  M1A                0                  2
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                    cls
clus                  0  1
  15Q GAIN MUTATED    3  0
  15Q GAIN WILD-TYPE 71 88
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      3    0
  15Q GAIN WILD-TYPE   71   88
        clus
vv       15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  FEMALE                3                 71
  MALE                  0                 88
[1] 2 2
[1] FALSE
D27V8, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     2   1
  15Q GAIN WILD-TYPE 141  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      2    1
  15Q GAIN WILD-TYPE  141   12
                                clus
vv                               15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         2                141
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D27V9, binary
                    cls
clus                   0   1
  15Q GAIN MUTATED     0   3
  15Q GAIN WILD-TYPE   6 153
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q GAIN MUTATED      0    3
  15Q GAIN WILD-TYPE    6  153
     clus
vv    15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  NO                 0                  6
  YES                3                153
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  15Q GAIN MUTATED     3   0   0   0
  15Q GAIN WILD-TYPE 118   2  12   3
D27V10, multiclass
    clus
vv   15Q GAIN MUTATED 15Q GAIN WILD-TYPE
  R0                3                118
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q GAIN MUTATED       0                         0     2
  15Q GAIN WILD-TYPE     1                         3    79
D27V12, multiclass
[1] "Remove cluster labels:" "15Q GAIN MUTATED"      
clus
  15Q GAIN MUTATED 15Q GAIN WILD-TYPE 
                 2                 83 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AH-6544 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-AH-6897         TCGA-AH-6903         TCGA-BM-6198 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6621 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-4745 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6154         TCGA-DC-6155         TCGA-DC-6156 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6157         TCGA-DC-6158         TCGA-DC-6160 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DC-6681         TCGA-DC-6682         TCGA-DC-6683 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DT-5265         TCGA-DY-A0XA         TCGA-DY-A1DC 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DD         TCGA-DY-A1DE         TCGA-DY-A1DF 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-DY-A1DG         TCGA-DY-A1H8         TCGA-EF-5830 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EF-5831         TCGA-EI-6506         TCGA-EI-6507 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6508         TCGA-EI-6509         TCGA-EI-6510 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6511         TCGA-EI-6512         TCGA-EI-6513 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6514         TCGA-EI-6881         TCGA-EI-6882 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6883         TCGA-EI-6884         TCGA-EI-6885 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-EI-6917         TCGA-EI-7002         TCGA-F5-6465 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"15Q GAIN WILD-TYPE" "15Q GAIN WILD-TYPE" 

Clustering(28) Variable = 16P GAIN MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                 0  1
  16P GAIN MUTATED   30  4
  16P GAIN WILD-TYPE 98 18
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                34                116 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
                 4                 18 
$`16P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3600 TCGA-AG-3726 
       17.95        37.74        15.39        20.02         6.05         7.99 
TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 
       17.03        19.99        36.03         0.99        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 
        9.07        12.00        31.00        38.96        38.04         0.72 
TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 
       10.19         6.97         9.37        60.03        11.01        12.99 
TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 
       12.00        10.06        24.13         0.49        17.69        16.31 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6863 
       37.51        14.86         0.39         0.76 

$`16P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       10.39        14.50         8.45        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 
       32.02        28.04        14.04         1.02        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.94         6.02        25.97        23.01        37.02         1.02 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00         0.49         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        1.81         6.05         6.05         4.73        13.97         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       10.98        15.02        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        51.48        32.61         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        31.30         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  16P GAIN MUTATED 16P GAIN WILD-TYPE 
              0.39               0.46 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
             60.03             129.27 
  16P GAIN MUTATED 16P GAIN WILD-TYPE 
            15.125             14.025 
[1] "0.4 - 60.0 (15.1)"  "0.5 - 129.3 (14.0)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P GAIN MUTATED         6        1         6         2         0         1
  16P GAIN WILD-TYPE      24        7        32         0         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P GAIN MUTATED            1         11          4        4         2
  16P GAIN WILD-TYPE          8         12         10       14         7
D28V3, multiclass
            clus
vv           16P GAIN MUTATED 16P GAIN WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  1                  7
  STAGE IIA                 6                 32
  STAGE IIB                 2                  0
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                1                  8
  STAGE IIIB               11                 12
  STAGE IIIC                4                 10
  STAGE IV                  4                 14
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16P GAIN MUTATED    2  7 25  5
  16P GAIN WILD-TYPE  7 22 84  9
D28V4, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  T1                2                  7
  T2                7                 22
  T3               25                 84
  T4                5                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16P GAIN MUTATED   16 14  8
  16P GAIN WILD-TYPE 67 31 24
D28V5, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  N0               16                 67
  N1               14                 31
  N2                8                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  16P GAIN MUTATED   28  6   0  4
  16P GAIN WILD-TYPE 95 16   2  9
D28V6, multiclass
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  M0                28                 95
  M1                 6                 16
  M1A                0                  2
  MX                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                    cls
clus                  0  1
  16P GAIN MUTATED   18 21
  16P GAIN WILD-TYPE 56 67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     18   21
  16P GAIN WILD-TYPE   56   67
        clus
vv       16P GAIN MUTATED 16P GAIN WILD-TYPE
  FEMALE               18                 56
  MALE                 21                 67
[1] 2 2
[1] FALSE
D28V8, binary
                    cls
clus                   0   1
  16P GAIN MUTATED    39   0
  16P GAIN WILD-TYPE 104  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED     39    0
  16P GAIN WILD-TYPE  104   13
                                clus
vv                               16P GAIN MUTATED 16P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        39                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D28V9, binary
                    cls
clus                   0   1
  16P GAIN MUTATED     3  36
  16P GAIN WILD-TYPE   3 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P GAIN MUTATED      3   36
  16P GAIN WILD-TYPE    3  120
     clus
vv    16P GAIN MUTATED 16P GAIN WILD-TYPE
  NO                 3                  3
  YES               36                120
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16P GAIN MUTATED   28  0  4  1
  16P GAIN WILD-TYPE 93  2  8  2
D28V10, multiclass
    clus
vv   16P GAIN MUTATED 16P GAIN WILD-TYPE
  R0               28                 93
  R1                0                  2
  R2                4                  8
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P GAIN MUTATED       0                         1    20
  16P GAIN WILD-TYPE     1                         2    61
D28V12, multiclass
                           clus
vv                          16P GAIN MUTATED 16P GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   20                 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(29) Variable = 16Q GAIN MUTATION ANALYSIS
D29V1, survival
                    sevent
clus2                 0  1
  16Q GAIN MUTATED   29  6
  16Q GAIN WILD-TYPE 99 16
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                35                115 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
                 6                 16 
$`16Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3890 
       17.95        37.74        10.39        15.39        20.02        17.03 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       19.99        36.03         0.99        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 
       12.00        31.00        38.96        38.04         0.72        10.19 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 
        9.37        60.03        11.01        12.99        12.00        10.06 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       24.13        51.48         0.49        17.69        16.31        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       14.86         0.39         0.66         0.69         0.76 

$`16Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       14.50         8.45        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        28.04        14.04         1.02        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        41.00         0.49         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        4.60         1.81         6.05         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 
       13.97         7.99        10.98        15.02        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        13.05         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24       129.27        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        31.30         1.02 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
              0.39               0.46 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             60.03             129.27 
  16Q GAIN MUTATED 16Q GAIN WILD-TYPE 
             15.39              14.01 
[1] "0.4 - 60.0 (15.4)"  "0.5 - 129.3 (14.0)"
[1] "hr=" "1.4"
D29V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q GAIN MUTATED         5        1         7         1         0         1
  16Q GAIN WILD-TYPE      25        7        31         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q GAIN MUTATED            1         10          4        5         3
  16Q GAIN WILD-TYPE          8         13         10       13         6
D29V3, multiclass
            clus
vv           16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  STAGE I                   5                 25
  STAGE II                  1                  7
  STAGE IIA                 7                 31
  STAGE IIB                 1                  1
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                1                  8
  STAGE IIIB               10                 13
  STAGE IIIC                4                 10
  STAGE IV                  5                 13
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  16Q GAIN MUTATED    2  6 27  4
  16Q GAIN WILD-TYPE  7 23 82 10
D29V4, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  T1                2                  7
  T2                6                 23
  T3               27                 82
  T4                4                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16Q GAIN MUTATED   15 15  8
  16Q GAIN WILD-TYPE 68 30 24
D29V5, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  N0               15                 68
  N1               15                 30
  N2                8                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  16Q GAIN MUTATED   26  8   0  4
  16Q GAIN WILD-TYPE 97 14   2  9
D29V6, multiclass
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  M0                26                 97
  M1                 8                 14
  M1A                0                  2
  MX                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                    cls
clus                  0  1
  16Q GAIN MUTATED   17 22
  16Q GAIN WILD-TYPE 57 66
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     17   22
  16Q GAIN WILD-TYPE   57   66
        clus
vv       16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  FEMALE               17                 57
  MALE                 22                 66
[1] 2 2
[1] FALSE
D29V8, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED    39   0
  16Q GAIN WILD-TYPE 104  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED     39    0
  16Q GAIN WILD-TYPE  104   13
                                clus
vv                               16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        39                104
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D29V9, binary
                    cls
clus                   0   1
  16Q GAIN MUTATED     3  36
  16Q GAIN WILD-TYPE   3 120
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q GAIN MUTATED      3   36
  16Q GAIN WILD-TYPE    3  120
     clus
vv    16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  NO                 3                  3
  YES               36                120
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  16Q GAIN MUTATED   29  0  3  1
  16Q GAIN WILD-TYPE 92  2  9  2
D29V10, multiclass
    clus
vv   16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  R0               29                 92
  R1                0                  2
  R2                3                  9
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q GAIN MUTATED       0                         2    22
  16Q GAIN WILD-TYPE     1                         1    59
D29V12, multiclass
                           clus
vv                          16Q GAIN MUTATED 16Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                2                  1
  WHITE                                   22                 59
[1] 3 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     8   0
  17P GAIN WILD-TYPE 120  22
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 8                142 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
                 0                 22 
$`17P GAIN MUTATED`
TCGA-AG-3587 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3882 TCGA-CI-6623 TCGA-DC-6154 
       46.03        15.95        19.99        19.99         9.37        12.00 
TCGA-DC-6682 TCGA-G5-6641 
       13.05        26.43 

$`17P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 
        7.07         1.02         2.01        24.00         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 
        2.01        50.04        12.03         6.05         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.46        18.28        55.76        47.08 

  17P GAIN MUTATED 17P GAIN WILD-TYPE 
              9.37               0.39 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
             46.03             129.27 
  17P GAIN MUTATED 17P GAIN WILD-TYPE 
            17.970             14.025 
[1] "9.4 - 46.0 (18.0)"  "0.4 - 129.3 (14.0)"
[1] "hr="     "2.7e+07"
D30V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P GAIN MUTATED         3        0         2         0         0         0
  17P GAIN WILD-TYPE      27        8        36         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P GAIN MUTATED            1          0          1        0         1
  17P GAIN WILD-TYPE          8         23         13       18         8
D30V3, multiclass
            clus
vv           17P GAIN MUTATED 17P GAIN WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  0                  8
  STAGE IIA                 2                 36
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                1                  8
  STAGE IIIB                0                 23
  STAGE IIIC                1                 13
  STAGE IV                  0                 18
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  17P GAIN MUTATED     2   2   3   1
  17P GAIN WILD-TYPE   7  27 106  13
D30V4, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  T1                2                  7
  T2                2                 27
  T3                3                106
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17P GAIN MUTATED    5  1  2
  17P GAIN WILD-TYPE 78 44 30
D30V5, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  N0                5                 78
  N1                1                 44
  N2                2                 30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17P GAIN MUTATED     6   1   0   1
  17P GAIN WILD-TYPE 117  21   2  12
D30V6, multiclass
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                    cls
clus                  0  1
  17P GAIN MUTATED    4  4
  17P GAIN WILD-TYPE 70 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      4    4
  17P GAIN WILD-TYPE   70   84
        clus
vv       17P GAIN MUTATED 17P GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  4                 84
[1] 2 2
[1] FALSE
D30V8, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     7   1
  17P GAIN WILD-TYPE 136  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      7    1
  17P GAIN WILD-TYPE  136   12
                                clus
vv                               17P GAIN MUTATED 17P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                136
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D30V9, binary
                    cls
clus                   0   1
  17P GAIN MUTATED     0   8
  17P GAIN WILD-TYPE   6 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P GAIN MUTATED      0    8
  17P GAIN WILD-TYPE    6  148
     clus
vv    17P GAIN MUTATED 17P GAIN WILD-TYPE
  NO                 0                  6
  YES                8                148
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17P GAIN MUTATED     7   0   0   0
  17P GAIN WILD-TYPE 114   2  12   3
D30V10, multiclass
    clus
vv   17P GAIN MUTATED 17P GAIN WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P GAIN MUTATED       0                         0     4
  17P GAIN WILD-TYPE     1                         3    77
D30V12, multiclass
                           clus
vv                          17P GAIN MUTATED 17P GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    4                 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(31) Variable = 17Q GAIN MUTATION ANALYSIS
D31V1, survival
                    sevent
clus2                  0   1
  17Q GAIN MUTATED    25   2
  17Q GAIN WILD-TYPE 103  20
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                27                123 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
                 2                 20 
$`17Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AG-3575 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 TCGA-AG-3609 
       17.23        12.00        46.03        34.03        15.95        19.99 
TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N 
       19.99        36.03        17.03        15.95         9.07        31.00 
TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 
        0.69         4.60         6.05        12.00        13.05        10.06 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 
       51.48        17.00        18.28        16.31        11.97         1.02 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.46        55.76        26.43 

$`17Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        2.01        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       32.02        19.99        28.04        14.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         1.02        12.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 
       38.04         0.49         1.45         0.72         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.99        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       15.02        36.00         7.10        30.05        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 
        0.49         2.40        20.55        19.96        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       14.86         0.39         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        0.76        18.28        47.08 

  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
              0.46               0.39 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             55.76             129.27 
  17Q GAIN MUTATED 17Q GAIN WILD-TYPE 
             16.31              13.97 
[1] "0.5 - 55.8 (16.3)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "2.1"
D31V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q GAIN MUTATED         4        1         8         0         0         1
  17Q GAIN WILD-TYPE      26        7        30         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q GAIN MUTATED            1          3          5        4         3
  17Q GAIN WILD-TYPE          8         20          9       14         6
D31V3, multiclass
            clus
vv           17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  STAGE I                   4                 26
  STAGE II                  1                  7
  STAGE IIA                 8                 30
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                1                  8
  STAGE IIIB                3                 20
  STAGE IIIC                5                  9
  STAGE IV                  4                 14
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q GAIN MUTATED    1  6 21  2
  17Q GAIN WILD-TYPE  8 23 88 12
D31V4, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               21                 88
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17Q GAIN MUTATED   15  7  8
  17Q GAIN WILD-TYPE 68 38 24
D31V5, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  N0               15                 68
  N1                7                 38
  N2                8                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17Q GAIN MUTATED    20   6   0   4
  17Q GAIN WILD-TYPE 103  16   2   9
D31V6, multiclass
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  M0                20                103
  M1                 6                 16
  M1A                0                  2
  MX                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                    cls
clus                  0  1
  17Q GAIN MUTATED   12 18
  17Q GAIN WILD-TYPE 62 70
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     12   18
  17Q GAIN WILD-TYPE   62   70
        clus
vv       17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  FEMALE               12                 62
  MALE                 18                 70
[1] 2 2
[1] FALSE
D31V8, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED    29   1
  17Q GAIN WILD-TYPE 114  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED     29    1
  17Q GAIN WILD-TYPE  114   12
                                clus
vv                               17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        29                114
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D31V9, binary
                    cls
clus                   0   1
  17Q GAIN MUTATED     0  30
  17Q GAIN WILD-TYPE   6 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q GAIN MUTATED      0   30
  17Q GAIN WILD-TYPE    6  126
     clus
vv    17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  NO                 0                  6
  YES               30                126
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17Q GAIN MUTATED   22  1  3  0
  17Q GAIN WILD-TYPE 99  1  9  3
D31V10, multiclass
    clus
vv   17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  R0               22                 99
  R1                1                  1
  R2                3                  9
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q GAIN MUTATED       0                         0    17
  17Q GAIN WILD-TYPE     1                         3    64
D31V12, multiclass
                           clus
vv                          17Q GAIN MUTATED 17Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   17                 64
[1] 3 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     5   2
  18P GAIN WILD-TYPE 123  20
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 7                143 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
                 2                 20 
$`18P GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-A01Y TCGA-AG-A02G TCGA-DT-5265 
       10.39        32.02         6.05        64.01        38.96         5.29 
TCGA-F5-6464 
        9.96 

$`18P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       20.02        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
       70.03        10.98        51.98        49.97         1.94        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  18P GAIN MUTATED 18P GAIN WILD-TYPE 
              5.29               0.39 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             64.01             129.27 
  18P GAIN MUTATED 18P GAIN WILD-TYPE 
             10.39              14.50 
[1] "5.3 - 64.0 (10.4)"  "0.4 - 129.3 (14.5)"
[1] "hr=" "1.4"
D32V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P GAIN MUTATED         0        2         1         0         0         1
  18P GAIN WILD-TYPE      30        6        37         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P GAIN MUTATED            0          0          2        2         0
  18P GAIN WILD-TYPE          9         23         12       16         9
D32V3, multiclass
            clus
vv           18P GAIN MUTATED 18P GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  2                  6
  STAGE IIA                 1                 37
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                0                  9
  STAGE IIIB                0                 23
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18P GAIN MUTATED     0   1   5   2
  18P GAIN WILD-TYPE   9  28 104  12
D32V4, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                5                104
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18P GAIN MUTATED    3  2  3
  18P GAIN WILD-TYPE 80 43 29
D32V5, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  N0                3                 80
  N1                2                 43
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18P GAIN MUTATED     5   1   0   2
  18P GAIN WILD-TYPE 118  21   2  11
D32V6, multiclass
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  M0                 5                118
  M1                 1                 21
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                    cls
clus                  0  1
  18P GAIN MUTATED    3  5
  18P GAIN WILD-TYPE 71 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      3    5
  18P GAIN WILD-TYPE   71   83
        clus
vv       18P GAIN MUTATED 18P GAIN WILD-TYPE
  FEMALE                3                 71
  MALE                  5                 83
[1] 2 2
[1] FALSE
D32V8, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     6   2
  18P GAIN WILD-TYPE 137  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      6    2
  18P GAIN WILD-TYPE  137   11
                                clus
vv                               18P GAIN MUTATED 18P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
D32V9, binary
                    cls
clus                   0   1
  18P GAIN MUTATED     1   7
  18P GAIN WILD-TYPE   5 149
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P GAIN MUTATED      1    7
  18P GAIN WILD-TYPE    5  149
     clus
vv    18P GAIN MUTATED 18P GAIN WILD-TYPE
  NO                 1                  5
  YES                7                149
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18P GAIN MUTATED     4   0   1   1
  18P GAIN WILD-TYPE 117   2  11   2
D32V10, multiclass
    clus
vv   18P GAIN MUTATED 18P GAIN WILD-TYPE
  R0                4                117
  R1                0                  2
  R2                1                 11
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P GAIN MUTATED       1                         0     3
  18P GAIN WILD-TYPE     0                         3    78
D32V12, multiclass
                           clus
vv                          18P GAIN MUTATED 18P GAIN WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    3                 78
[1] 3 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     3   2
  18Q GAIN WILD-TYPE 125  20
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 5                145 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
                 2                 20 
$`18Q GAIN MUTATED`
TCGA-AF-6672 TCGA-AG-3600 TCGA-AG-A02G TCGA-DT-5265 TCGA-F5-6464 
       10.39         6.05        38.96         5.29         9.96 

$`18Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              5.29               0.39 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
             38.96             129.27 
  18Q GAIN MUTATED 18Q GAIN WILD-TYPE 
              9.96              14.86 
[1] "5.3 - 39.0 (10.0)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "4.5"
D33V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q GAIN MUTATED         0        1         0         0         0         1
  18Q GAIN WILD-TYPE      30        7        38         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q GAIN MUTATED            0          0          2        2         0
  18Q GAIN WILD-TYPE          9         23         12       16         9
D33V3, multiclass
            clus
vv           18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  1                  7
  STAGE IIA                 0                 38
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                0                  9
  STAGE IIIB                0                 23
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  18Q GAIN MUTATED     0   1   3   2
  18Q GAIN WILD-TYPE   9  28 106  12
D33V4, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                3                106
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18Q GAIN MUTATED    1  2  3
  18Q GAIN WILD-TYPE 82 43 29
D33V5, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  N0                1                 82
  N1                2                 43
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18Q GAIN MUTATED     3   1   0   2
  18Q GAIN WILD-TYPE 120  21   2  11
D33V6, multiclass
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  M0                 3                120
  M1                 1                 21
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                    cls
clus                  0  1
  18Q GAIN MUTATED    1  5
  18Q GAIN WILD-TYPE 73 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE   73   83
        clus
vv       18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  FEMALE                1                 73
  MALE                  5                 83
[1] 2 2
[1] FALSE
D33V8, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     5   1
  18Q GAIN WILD-TYPE 138  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      5    1
  18Q GAIN WILD-TYPE  138   12
                                clus
vv                               18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         5                138
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D33V9, binary
                    cls
clus                   0   1
  18Q GAIN MUTATED     1   5
  18Q GAIN WILD-TYPE   5 151
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q GAIN MUTATED      1    5
  18Q GAIN WILD-TYPE    5  151
     clus
vv    18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  NO                 1                  5
  YES                5                151
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q GAIN MUTATED     2   0   1   1
  18Q GAIN WILD-TYPE 119   2  11   2
D33V10, multiclass
    clus
vv   18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  R0                2                119
  R1                0                  2
  R2                1                 11
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q GAIN MUTATED       1                         0     3
  18Q GAIN WILD-TYPE     0                         3    78
D33V12, multiclass
                           clus
vv                          18Q GAIN MUTATED 18Q GAIN WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    3                 78
[1] 3 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    24   4
  19P GAIN WILD-TYPE 104  18
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                28                122 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
                 4                 18 
$`19P GAIN MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 
       17.95        17.23         1.02        46.03         6.05        19.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A014 
        0.99        19.99         1.02        36.03         1.02        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-BM-6198 TCGA-CI-6619 
       12.00        31.00         1.94        38.04        10.19         6.05 
TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 
       10.98        12.00        36.00        13.05       129.27        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6863 
       17.69        16.31        13.64         0.76 

$`19P GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       24.13        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        1.02        32.98         0.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72         4.60         1.81         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        13.97        15.02         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.06         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         0.49         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  19P GAIN MUTATED 19P GAIN WILD-TYPE 
              0.76               0.39 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            129.27             126.44 
  19P GAIN MUTATED 19P GAIN WILD-TYPE 
            14.795             14.270 
[1] "0.8 - 129.3 (14.8)" "0.4 - 126.4 (14.3)"
[1] "hr=" "1.2"
D34V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P GAIN MUTATED         6        1         7         0         0         1
  19P GAIN WILD-TYPE      24        7        31         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P GAIN MUTATED            0          6          3        6         1
  19P GAIN WILD-TYPE          9         17         11       12         8
D34V3, multiclass
            clus
vv           19P GAIN MUTATED 19P GAIN WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  1                  7
  STAGE IIA                 7                 31
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                0                  9
  STAGE IIIB                6                 17
  STAGE IIIC                3                 11
  STAGE IV                  6                 12
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P GAIN MUTATED    0  7 20  4
  19P GAIN WILD-TYPE  9 22 89 10
D34V4, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  T1                0                  9
  T2                7                 22
  T3               20                 89
  T4                4                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19P GAIN MUTATED   15 10  6
  19P GAIN WILD-TYPE 68 35 26
D34V5, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  N0               15                 68
  N1               10                 35
  N2                6                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19P GAIN MUTATED    22   7   0   1
  19P GAIN WILD-TYPE 101  15   2  12
D34V6, multiclass
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  M0                22                101
  M1                 7                 15
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                    cls
clus                  0  1
  19P GAIN MUTATED   16 15
  19P GAIN WILD-TYPE 58 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     16   15
  19P GAIN WILD-TYPE   58   73
        clus
vv       19P GAIN MUTATED 19P GAIN WILD-TYPE
  FEMALE               16                 58
  MALE                 15                 73
[1] 2 2
[1] FALSE
D34V8, binary
                    cls
clus                   0   1
  19P GAIN MUTATED    31   0
  19P GAIN WILD-TYPE 112  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED     31    0
  19P GAIN WILD-TYPE  112   13
                                clus
vv                               19P GAIN MUTATED 19P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        31                112
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D34V9, binary
                    cls
clus                   0   1
  19P GAIN MUTATED     1  30
  19P GAIN WILD-TYPE   5 126
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P GAIN MUTATED      1   30
  19P GAIN WILD-TYPE    5  126
     clus
vv    19P GAIN MUTATED 19P GAIN WILD-TYPE
  NO                 1                  5
  YES               30                126
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  19P GAIN MUTATED   24  1  3  0
  19P GAIN WILD-TYPE 97  1  9  3
D34V10, multiclass
    clus
vv   19P GAIN MUTATED 19P GAIN WILD-TYPE
  R0               24                 97
  R1                1                  1
  R2                3                  9
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P GAIN MUTATED       0                         1    14
  19P GAIN WILD-TYPE     1                         2    67
D34V12, multiclass
                           clus
vv                          19P GAIN MUTATED 19P GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   14                 67
[1] 3 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   2
  19Q GAIN WILD-TYPE 104  20
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                26                124 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
                 2                 20 
$`19Q GAIN MUTATED`
TCGA-AF-2689 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3896 
       17.95        46.03        19.99         0.99        19.99         1.02 
TCGA-AG-4007 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N 
        1.02        15.95        36.03         9.07        12.00        31.00 
TCGA-AG-A026 TCGA-AG-A032 TCGA-BM-6198 TCGA-CI-6619 TCGA-CL-4957 TCGA-DC-6154 
        1.94        38.04        10.19         6.05        13.97        12.00 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6514 
       36.00        13.05       129.27        20.55        17.69        16.31 
TCGA-EI-6885 TCGA-F5-6863 
       13.64         0.76 

$`19Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
        1.02         2.01        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       23.01        37.02         1.02        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       51.98        49.97        38.96        61.97        41.00         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
        1.45         0.69         0.72         4.60         1.81         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37         4.73        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       11.01        15.02        12.99        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         0.53         1.12         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
              0.76               0.39 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
            129.27             126.44 
  19Q GAIN MUTATED 19Q GAIN WILD-TYPE 
             14.96              14.27 
[1] "0.8 - 129.3 (15.0)" "0.4 - 126.4 (14.3)"
[1] "hr=" "1.8"
D35V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q GAIN MUTATED         7        1         6         0         0         1
  19Q GAIN WILD-TYPE      23        7        32         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q GAIN MUTATED            1          6          1        6         1
  19Q GAIN WILD-TYPE          8         17         13       12         8
D35V3, multiclass
            clus
vv           19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  1                  7
  STAGE IIA                 6                 32
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                1                  8
  STAGE IIIB                6                 17
  STAGE IIIC                1                 13
  STAGE IV                  6                 12
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q GAIN MUTATED    1  7 17  5
  19Q GAIN WILD-TYPE  8 22 92  9
D35V4, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  T1                1                  8
  T2                7                 22
  T3               17                 92
  T4                5                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19Q GAIN MUTATED   15 10  5
  19Q GAIN WILD-TYPE 68 35 27
D35V5, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  N0               15                 68
  N1               10                 35
  N2                5                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19Q GAIN MUTATED    21   7   0   1
  19Q GAIN WILD-TYPE 102  15   2  12
D35V6, multiclass
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  M0                21                102
  M1                 7                 15
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                    cls
clus                  0  1
  19Q GAIN MUTATED   15 15
  19Q GAIN WILD-TYPE 59 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     15   15
  19Q GAIN WILD-TYPE   59   73
        clus
vv       19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  FEMALE               15                 59
  MALE                 15                 73
[1] 2 2
[1] FALSE
D35V8, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED    30   0
  19Q GAIN WILD-TYPE 113  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED     30    0
  19Q GAIN WILD-TYPE  113   13
                                clus
vv                               19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                113
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D35V9, binary
                    cls
clus                   0   1
  19Q GAIN MUTATED     1  29
  19Q GAIN WILD-TYPE   5 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q GAIN MUTATED      1   29
  19Q GAIN WILD-TYPE    5  127
     clus
vv    19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  NO                 1                  5
  YES               29                127
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q GAIN MUTATED    21   1   4   0
  19Q GAIN WILD-TYPE 100   1   8   3
D35V10, multiclass
    clus
vv   19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  R0               21                100
  R1                1                  1
  R2                4                  8
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q GAIN MUTATED       0                         1    12
  19Q GAIN WILD-TYPE     1                         2    69
D35V12, multiclass
                           clus
vv                          19Q GAIN MUTATED 19Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   12                 69
[1] 3 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   82 15
  20P GAIN WILD-TYPE 46  7
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                97                 53 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
                15                  7 
$`20P GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        19.10        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
        8.45        20.02        10.39         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        2.01        24.00         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       12.03        15.95        19.99        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        1.02         0.99         0.99         1.02        36.95        17.03 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       14.04         1.02        17.03         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A023 TCGA-AG-A02X 
       37.02        15.95        36.03         9.07        51.98        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 
        1.81        10.19         6.05         6.97         9.37        13.97 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       10.98        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC 
       36.00         7.10        30.05        12.95       126.44        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
      129.27        24.13        32.61         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
       17.00        18.28        17.69        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       13.64        11.97         9.96        37.51         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 
       47.08 

$`20P GAIN WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3574 
       43.04        13.55        12.72        14.50        15.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
       12.00        32.02         2.01         6.05         0.99         7.99 
TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3902 TCGA-AG-4022 
       32.98        19.99        13.02        35.01        32.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       20.98        13.94         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        49.97         1.94        38.96        61.97 
TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6682 
        6.05         4.73        60.03         7.99        11.01        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6507 
       10.06         5.29        57.24        51.48         0.49        19.96 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       15.85        16.34        16.41         8.61        17.46         8.45 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6641 
       31.30        14.86         0.69         0.46        26.43 

  20P GAIN MUTATED 20P GAIN WILD-TYPE 
              0.39               0.46 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
            129.27              70.03 
  20P GAIN MUTATED 20P GAIN WILD-TYPE 
             14.04              14.50 
[1] "0.4 - 129.3 (14.0)" "0.5 - 70.0 (14.5)" 
[1] "hr=" "1.6"
D36V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P GAIN MUTATED        20        0        26         1         2         4
  20P GAIN WILD-TYPE      10        8        12         1         0         1
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P GAIN MUTATED            6         14          9       14         4
  20P GAIN WILD-TYPE          3          9          5        4         5
D36V3, multiclass
            clus
vv           20P GAIN MUTATED 20P GAIN WILD-TYPE
  STAGE I                  20                 10
  STAGE II                  0                  8
  STAGE IIA                26                 12
  STAGE IIB                 1                  1
  STAGE IIC                 2                  0
  STAGE III                 4                  1
  STAGE IIIA                6                  3
  STAGE IIIB               14                  9
  STAGE IIIC                9                  5
  STAGE IV                 14                  4
  STAGE IVA                 4                  5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P GAIN MUTATED    5 20 70  8
  20P GAIN WILD-TYPE  4  9 39  6
D36V4, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  T1                5                  4
  T2               20                  9
  T3               70                 39
  T4                8                  6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20P GAIN MUTATED   51 27 24
  20P GAIN WILD-TYPE 32 18  8
D36V5, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  N0               51                 32
  N1               27                 18
  N2               24                  8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  20P GAIN MUTATED   77 15   2  8
  20P GAIN WILD-TYPE 46  7   0  5
D36V6, multiclass
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  M0                77                 46
  M1                15                  7
  M1A                2                  0
  MX                 8                  5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   44 60
  20P GAIN WILD-TYPE 30 28
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     44   60
  20P GAIN WILD-TYPE   30   28
        clus
vv       20P GAIN MUTATED 20P GAIN WILD-TYPE
  FEMALE               44                 30
  MALE                 60                 28
[1] 2 2
[1] FALSE
D36V8, binary
                    cls
clus                  0  1
  20P GAIN MUTATED   97  4
  20P GAIN WILD-TYPE 46  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED     97    4
  20P GAIN WILD-TYPE   46    9
                                clus
vv                               20P GAIN MUTATED 20P GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        97                 46
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
D36V9, binary
                    cls
clus                   0   1
  20P GAIN MUTATED     4 100
  20P GAIN WILD-TYPE   2  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P GAIN MUTATED      4  100
  20P GAIN WILD-TYPE    2   56
     clus
vv    20P GAIN MUTATED 20P GAIN WILD-TYPE
  NO                 4                  2
  YES              100                 56
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  20P GAIN MUTATED   78  1  7  0
  20P GAIN WILD-TYPE 43  1  5  3
D36V10, multiclass
    clus
vv   20P GAIN MUTATED 20P GAIN WILD-TYPE
  R0               78                 43
  R1                1                  1
  R2                7                  5
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P GAIN MUTATED       0                         3    54
  20P GAIN WILD-TYPE     1                         0    27
D36V12, multiclass
                           clus
vv                          20P GAIN MUTATED 20P GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   54                 27
[1] 3 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   111  21
  20Q GAIN WILD-TYPE  17   1
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
               132                 18 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
                21                  1 
$`20Q GAIN MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       70.03        10.98        51.98         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

$`20Q GAIN WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       13.55        12.72        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02N 
       32.98        13.02        20.98        64.01        49.97        61.97 
TCGA-CL-5917 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       60.03         5.29        19.96         8.61        17.46         8.45 

  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
              0.39               2.01 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            129.27              64.01 
  20Q GAIN MUTATED 20Q GAIN WILD-TYPE 
            14.270             15.505 
[1] "0.4 - 129.3 (14.3)" "2.0 - 64.0 (15.5)" 
[1] "hr=" "4.9"
D37V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20Q GAIN MUTATED        26        4        31         2         2         5
  20Q GAIN WILD-TYPE       4        4         7         0         0         0
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20Q GAIN MUTATED            8         23         12       17         8
  20Q GAIN WILD-TYPE          1          0          2        1         1
D37V3, multiclass
            clus
vv           20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  STAGE I                  26                  4
  STAGE II                  4                  4
  STAGE IIA                31                  7
  STAGE IIB                 2                  0
  STAGE IIC                 2                  0
  STAGE III                 5                  0
  STAGE IIIA                8                  1
  STAGE IIIB               23                  0
  STAGE IIIC               12                  2
  STAGE IV                 17                  1
  STAGE IVA                 8                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20Q GAIN MUTATED    7 27 94 13
  20Q GAIN WILD-TYPE  2  2 15  1
D37V4, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  T1                7                  2
  T2               27                  2
  T3               94                 15
  T4               13                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20Q GAIN MUTATED   68 44 28
  20Q GAIN WILD-TYPE 15  1  4
D37V5, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  N0               68                 15
  N1               44                  1
  N2               28                  4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  20Q GAIN MUTATED   105  21   2  12
  20Q GAIN WILD-TYPE  18   1   0   1
D37V6, multiclass
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  M0               105                 18
  M1                21                  1
  M1A                2                  0
  MX                12                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                    cls
clus                  0  1
  20Q GAIN MUTATED   64 78
  20Q GAIN WILD-TYPE 10 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED     64   78
  20Q GAIN WILD-TYPE   10   10
        clus
vv       20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  FEMALE               64                 10
  MALE                 78                 10
[1] 2 2
[1] FALSE
D37V8, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED   131   7
  20Q GAIN WILD-TYPE  12   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED    131    7
  20Q GAIN WILD-TYPE   12    6
                                clus
vv                               20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       131                 12
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[1] 2 2
[1] FALSE
D37V9, binary
                    cls
clus                   0   1
  20Q GAIN MUTATED     5 137
  20Q GAIN WILD-TYPE   1  19
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20Q GAIN MUTATED      5  137
  20Q GAIN WILD-TYPE    1   19
     clus
vv    20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  NO                 5                  1
  YES              137                 19
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20Q GAIN MUTATED   105   2  11   1
  20Q GAIN WILD-TYPE  16   0   1   2
D37V10, multiclass
    clus
vv   20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  R0              105                 16
  R1                2                  0
  R2               11                  1
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20Q GAIN MUTATED       0                         3    74
  20Q GAIN WILD-TYPE     1                         0     7
D37V12, multiclass
                           clus
vv                          20Q GAIN MUTATED 20Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   74                  7
[1] 3 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     7   0
  21Q GAIN WILD-TYPE 121  22
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 7                143 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
                 0                 22 
$`21Q GAIN MUTATED`
TCGA-AG-3612 TCGA-AG-3732 TCGA-AG-A011 TCGA-AH-6644 TCGA-CI-6623 TCGA-EF-5830 
       19.99        32.98        37.02         0.72         9.37         0.49 
TCGA-EI-6885 
       13.64 

$`21Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
              0.49               0.39 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             37.02             129.27 
  21Q GAIN MUTATED 21Q GAIN WILD-TYPE 
             13.64              14.50 
[1] "0.5 - 37.0 (13.6)"  "0.4 - 129.3 (14.5)"
[1] "hr="     "2.6e+07"
D38V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q GAIN MUTATED         2        0         2         1         0         0
  21Q GAIN WILD-TYPE      28        8        36         1         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q GAIN MUTATED            0          2          0        2         0
  21Q GAIN WILD-TYPE          9         21         14       16         9
D38V3, multiclass
            clus
vv           21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  0                  8
  STAGE IIA                 2                 36
  STAGE IIB                 1                  1
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                2                 21
  STAGE IIIC                0                 14
  STAGE IV                  2                 16
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  21Q GAIN MUTATED     1   1   7   1
  21Q GAIN WILD-TYPE   8  28 102  13
D38V4, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  T1                1                  8
  T2                1                 28
  T3                7                102
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  21Q GAIN MUTATED    5  3  1
  21Q GAIN WILD-TYPE 78 42 31
D38V5, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  N0                5                 78
  N1                3                 42
  N2                1                 31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  21Q GAIN MUTATED     7   2   0   1
  21Q GAIN WILD-TYPE 116  20   2  12
D38V6, multiclass
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  M0                 7                116
  M1                 2                 20
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                    cls
clus                  0  1
  21Q GAIN MUTATED    5  5
  21Q GAIN WILD-TYPE 69 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      5    5
  21Q GAIN WILD-TYPE   69   83
        clus
vv       21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  FEMALE                5                 69
  MALE                  5                 83
[1] 2 2
[1] FALSE
D38V8, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED    10   0
  21Q GAIN WILD-TYPE 133  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED     10    0
  21Q GAIN WILD-TYPE  133   13
                                clus
vv                               21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                        10                133
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D38V9, binary
                    cls
clus                   0   1
  21Q GAIN MUTATED     0  10
  21Q GAIN WILD-TYPE   6 146
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q GAIN MUTATED      0   10
  21Q GAIN WILD-TYPE    6  146
     clus
vv    21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  NO                 0                  6
  YES               10                146
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  21Q GAIN MUTATED     7   0   1   0
  21Q GAIN WILD-TYPE 114   2  11   3
D38V10, multiclass
    clus
vv   21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q GAIN MUTATED       0                         0     4
  21Q GAIN WILD-TYPE     1                         3    77
D38V12, multiclass
                           clus
vv                          21Q GAIN MUTATED 21Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    4                 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(39) Variable = 22Q GAIN MUTATION ANALYSIS
D39V1, survival
                    sevent
clus2                  0   1
  22Q GAIN MUTATED     6   3
  22Q GAIN WILD-TYPE 122  19
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 9                141 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
                 3                 19 
$`22Q GAIN MUTATED`
TCGA-AF-2690 TCGA-AG-3582 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3893 TCGA-AG-A00Y 
       17.23         1.02        19.99        19.99        35.01        23.01 
TCGA-AH-6897 TCGA-CI-6623 TCGA-DY-A1DF 
        4.60         9.37        24.13 

$`22Q GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 
       50.04        12.03         6.05         0.99        15.95         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        13.02        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 
       38.04         0.49         1.45         0.69         0.72         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       10.19         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
              1.02               0.39 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             35.01             129.27 
  22Q GAIN MUTATED 22Q GAIN WILD-TYPE 
             19.99              14.01 
[1] "1.0 - 35.0 (20.0)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "3.6"
D39V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q GAIN MUTATED         2        0         1         0         0         0
  22Q GAIN WILD-TYPE      28        8        37         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q GAIN MUTATED            0          2          3        1         0
  22Q GAIN WILD-TYPE          9         21         11       17         9
D39V3, multiclass
            clus
vv           22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  0                  8
  STAGE IIA                 1                 37
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                2                 21
  STAGE IIIC                3                 11
  STAGE IV                  1                 17
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  22Q GAIN MUTATED     1   1   7   0
  22Q GAIN WILD-TYPE   8  28 102  14
D39V4, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  T1                1                  8
  T2                1                 28
  T3                7                102
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  22Q GAIN MUTATED    3  3  3
  22Q GAIN WILD-TYPE 80 42 29
D39V5, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  N0                3                 80
  N1                3                 42
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  22Q GAIN MUTATED     8   1   0   0
  22Q GAIN WILD-TYPE 115  21   2  13
D39V6, multiclass
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  M0                 8                115
  M1                 1                 21
  M1A                0                  2
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                    cls
clus                  0  1
  22Q GAIN MUTATED    4  5
  22Q GAIN WILD-TYPE 70 83
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      4    5
  22Q GAIN WILD-TYPE   70   83
        clus
vv       22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  FEMALE                4                 70
  MALE                  5                 83
[1] 2 2
[1] FALSE
D39V8, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     9   0
  22Q GAIN WILD-TYPE 134  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      9    0
  22Q GAIN WILD-TYPE  134   13
                                clus
vv                               22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                         9                134
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D39V9, binary
                    cls
clus                   0   1
  22Q GAIN MUTATED     0   9
  22Q GAIN WILD-TYPE   6 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q GAIN MUTATED      0    9
  22Q GAIN WILD-TYPE    6  147
     clus
vv    22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  NO                 0                  6
  YES                9                147
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  22Q GAIN MUTATED     6   0   1   0
  22Q GAIN WILD-TYPE 115   2  11   3
D39V10, multiclass
    clus
vv   22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  R0                6                115
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q GAIN MUTATED       0                         0     4
  22Q GAIN WILD-TYPE     1                         3    77
D39V12, multiclass
                           clus
vv                          22Q GAIN MUTATED 22Q GAIN WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    4                 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(40) Variable = XQ GAIN MUTATION ANALYSIS
D40V1, survival
                   sevent
clus2                 0   1
  XQ GAIN MUTATED    24   5
  XQ GAIN WILD-TYPE 104  17
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
               29               121 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
                5                17 
$`XQ GAIN MUTATED`
TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3594 TCGA-AG-3609 
       13.55        10.39         8.45        20.02         2.01        19.99 
TCGA-AG-3612 TCGA-AG-3893 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 
       19.99        35.01        28.04         1.02         0.99        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 
       36.03         9.07        38.04         0.72         9.37        60.03 
TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1DD TCGA-EI-6510 TCGA-EI-6512 
       10.98        12.00        15.02        57.24        18.28        17.69 
TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
       13.64         9.96        37.51         0.39         0.76 

$`XQ GAIN WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       37.74        14.50        15.39        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       19.99        36.03        14.04        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L 
        6.02        25.97        23.01        37.02         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        41.00         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        6.97         4.73        13.97         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        13.97        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE 
       13.05        10.06         5.29       126.44        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        15.85        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        8.45        31.30        14.86         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
             0.39              0.46 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            60.03            129.27 
  XQ GAIN MUTATED XQ GAIN WILD-TYPE 
            13.64             14.50 
[1] "0.4 - 60.0 (13.6)"  "0.5 - 129.3 (14.5)"
[1] "hr=" "1.3"
D40V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ GAIN MUTATED         4        1         6         0         0         0
  XQ GAIN WILD-TYPE      26        7        32         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ GAIN MUTATED            1          8          4        4         3
  XQ GAIN WILD-TYPE          8         15         10       14         6
D40V3, multiclass
            clus
vv           XQ GAIN MUTATED XQ GAIN WILD-TYPE
  STAGE I                  4                26
  STAGE II                 1                 7
  STAGE IIA                6                32
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               1                 8
  STAGE IIIB               8                15
  STAGE IIIC               4                10
  STAGE IV                 4                14
  STAGE IVA                3                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ GAIN MUTATED    2  4 20  6
  XQ GAIN WILD-TYPE  7 25 89  8
D40V4, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  T1               2                 7
  T2               4                25
  T3              20                89
  T4               6                 8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  XQ GAIN MUTATED   12 11  8
  XQ GAIN WILD-TYPE 71 34 24
D40V5, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  N0              12                71
  N1              11                34
  N2               8                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  XQ GAIN MUTATED    23   5   1   3
  XQ GAIN WILD-TYPE 100  17   1  10
D40V6, multiclass
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  M0               23               100
  M1                5                17
  M1A               1                 1
  MX                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                   cls
clus                 0  1
  XQ GAIN MUTATED   18 14
  XQ GAIN WILD-TYPE 56 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     18   14
  XQ GAIN WILD-TYPE   56   74
        clus
vv       XQ GAIN MUTATED XQ GAIN WILD-TYPE
  FEMALE              18                56
  MALE                14                74
[1] 2 2
[1] FALSE
D40V8, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED    29   1
  XQ GAIN WILD-TYPE 114  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED     29    1
  XQ GAIN WILD-TYPE  114   12
                                clus
vv                               XQ GAIN MUTATED XQ GAIN WILD-TYPE
  RECTAL ADENOCARCINOMA                       29               114
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D40V9, binary
                   cls
clus                  0   1
  XQ GAIN MUTATED     0  32
  XQ GAIN WILD-TYPE   6 124
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ GAIN MUTATED      0   32
  XQ GAIN WILD-TYPE    6  124
     clus
vv    XQ GAIN MUTATED XQ GAIN WILD-TYPE
  NO                0                 6
  YES              32               124
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  XQ GAIN MUTATED   24  0  3  1
  XQ GAIN WILD-TYPE 97  2  9  2
D40V10, multiclass
    clus
vv   XQ GAIN MUTATED XQ GAIN WILD-TYPE
  R0              24                97
  R1               0                 2
  R2               3                 9
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ GAIN MUTATED       0                         1    17
  XQ GAIN WILD-TYPE     1                         2    64
D40V12, multiclass
                           clus
vv                          XQ GAIN MUTATED XQ GAIN WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                  17                64
[1] 3 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   36  6
  1P LOSS WILD-TYPE 92 16
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
               42               108 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
                6                16 
$`1P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3584 
       24.13        17.23        14.50        15.39         1.02        24.00 
TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 
       34.03        29.98         1.02        19.99         1.02         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y 
       48.03        19.99        28.04        36.03        25.97        23.01 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       12.00        70.03        38.96        38.04         0.49         0.69 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       10.19         9.37         4.73        11.01        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 
       36.00        30.05       126.44       129.27         0.49        20.55 
TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       15.85        11.97        14.86         1.02         0.69        47.08 

$`1P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       10.39         8.45        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       32.02         8.02         7.07         2.01         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 
       19.99        19.99         7.99         0.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       32.02        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
        1.94        61.97        41.00         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
        1.81         6.05         6.05         6.97        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
        7.99        10.98        15.02        12.00        15.02         7.10 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48        32.61         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 
        9.96        37.51        31.30         0.39         0.66         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.12         0.76         0.46        18.28        55.76        26.43 

  1P LOSS MUTATED 1P LOSS WILD-TYPE 
             0.49              0.39 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
           129.27             64.01 
  1P LOSS MUTATED 1P LOSS WILD-TYPE 
            16.54             13.79 
[1] "0.5 - 129.3 (16.5)" "0.4 - 64.0 (13.8)" 
[1] "hr=" "1.2"
D41V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1P LOSS MUTATED         8        1        10         1         0         1
  1P LOSS WILD-TYPE      22        7        28         1         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1P LOSS MUTATED            1          8          5        5         2
  1P LOSS WILD-TYPE          8         15          9       13         7
D41V3, multiclass
            clus
vv           1P LOSS MUTATED 1P LOSS WILD-TYPE
  STAGE I                  8                22
  STAGE II                 1                 7
  STAGE IIA               10                28
  STAGE IIB                1                 1
  STAGE IIC                0                 2
  STAGE III                1                 4
  STAGE IIIA               1                 8
  STAGE IIIB               8                15
  STAGE IIIC               5                 9
  STAGE IV                 5                13
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1P LOSS MUTATED    1  9 30  3
  1P LOSS WILD-TYPE  8 20 79 11
D41V4, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  T1               1                 8
  T2               9                20
  T3              30                79
  T4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1P LOSS MUTATED   20 15  8
  1P LOSS WILD-TYPE 63 30 24
D41V5, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  N0              20                63
  N1              15                30
  N2               8                24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  1P LOSS MUTATED   32  7   0  3
  1P LOSS WILD-TYPE 91 15   2 10
D41V6, multiclass
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  M0               32                91
  M1                7                15
  M1A               0                 2
  MX                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                   cls
clus                 0  1
  1P LOSS MUTATED   17 27
  1P LOSS WILD-TYPE 57 61
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     17   27
  1P LOSS WILD-TYPE   57   61
        clus
vv       1P LOSS MUTATED 1P LOSS WILD-TYPE
  FEMALE              17                57
  MALE                27                61
[1] 2 2
[1] FALSE
D41V8, binary
                   cls
clus                  0   1
  1P LOSS MUTATED    42   0
  1P LOSS WILD-TYPE 101  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED     42    0
  1P LOSS WILD-TYPE  101   13
                                clus
vv                               1P LOSS MUTATED 1P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       42               101
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D41V9, binary
                   cls
clus                  0   1
  1P LOSS MUTATED     3  41
  1P LOSS WILD-TYPE   3 115
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1P LOSS MUTATED      3   41
  1P LOSS WILD-TYPE    3  115
     clus
vv    1P LOSS MUTATED 1P LOSS WILD-TYPE
  NO                3                 3
  YES              41               115
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  1P LOSS MUTATED   30  0  4  0
  1P LOSS WILD-TYPE 91  2  8  3
D41V10, multiclass
    clus
vv   1P LOSS MUTATED 1P LOSS WILD-TYPE
  R0              30                91
  R1               0                 2
  R2               4                 8
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1P LOSS MUTATED       0                         2    23
  1P LOSS WILD-TYPE     1                         1    58
D41V12, multiclass
                           clus
vv                          1P LOSS MUTATED 1P LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  23                58
[1] 3 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    20   4
  1Q LOSS WILD-TYPE 108  18
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
               24               126 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
                4                18 
$`1Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3882 
       24.13        14.50         1.02        24.00         1.02        19.99 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y 
        1.02         1.02        19.99        36.03        25.97        23.01 
TCGA-AG-A01L TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6157 
       12.00        10.19         4.73        11.01        12.99        36.00 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-F5-6702 TCGA-G5-6572 
        0.49        20.55        15.85        11.97        14.86        47.08 

$`1Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        0.99        29.98        32.98         0.99         0.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
        7.99        10.98        15.02        12.00        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        1.12         0.76         0.46        18.28        55.76        26.43 

  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
             0.49              0.39 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
            47.08            129.27 
  1Q LOSS MUTATED 1Q LOSS WILD-TYPE 
           14.680            14.025 
[1] "0.5 - 47.1 (14.7)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.7"
D42V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  1Q LOSS MUTATED         6        0         4         1         0         1
  1Q LOSS WILD-TYPE      24        8        34         1         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  1Q LOSS MUTATED            0          5          1        4         2
  1Q LOSS WILD-TYPE          9         18         13       14         7
D42V3, multiclass
            clus
vv           1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 0                 8
  STAGE IIA                4                34
  STAGE IIB                1                 1
  STAGE IIC                0                 2
  STAGE III                1                 4
  STAGE IIIA               0                 9
  STAGE IIIB               5                18
  STAGE IIIC               1                13
  STAGE IV                 4                14
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  1Q LOSS MUTATED    0  6 16  2
  1Q LOSS WILD-TYPE  9 23 93 12
D42V4, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  T1               0                 9
  T2               6                23
  T3              16                93
  T4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  1Q LOSS MUTATED   11  9  4
  1Q LOSS WILD-TYPE 72 36 28
D42V5, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  N0              11                72
  N1               9                36
  N2               4                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  1Q LOSS MUTATED    16   5   0   2
  1Q LOSS WILD-TYPE 107  17   2  11
D42V6, multiclass
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  M0               16               107
  M1                5                17
  M1A               0                 2
  MX                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                   cls
clus                 0  1
  1Q LOSS MUTATED    7 18
  1Q LOSS WILD-TYPE 67 70
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      7   18
  1Q LOSS WILD-TYPE   67   70
        clus
vv       1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  FEMALE               7                67
  MALE                18                70
[1] 2 2
[1] FALSE
D42V8, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED    24   0
  1Q LOSS WILD-TYPE 119  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED     24    0
  1Q LOSS WILD-TYPE  119   13
                                clus
vv                               1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       24               119
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D42V9, binary
                   cls
clus                  0   1
  1Q LOSS MUTATED     2  23
  1Q LOSS WILD-TYPE   4 133
[1] "tbl2"
                   cls
clus                [,1] [,2]
  1Q LOSS MUTATED      2   23
  1Q LOSS WILD-TYPE    4  133
     clus
vv    1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  NO                2                 4
  YES              23               133
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  1Q LOSS MUTATED    19   0   3   0
  1Q LOSS WILD-TYPE 102   2   9   3
D42V10, multiclass
    clus
vv   1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  R0              19               102
  R1               0                 2
  R2               3                 9
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  1Q LOSS MUTATED       0                         2    12
  1Q LOSS WILD-TYPE     1                         1    69
D42V12, multiclass
                           clus
vv                          1Q LOSS MUTATED 1Q LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  12                69
[1] 3 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     8   1
  2P LOSS WILD-TYPE 120  21
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                9               141 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
                1                21 
$`2P LOSS MUTATED`
TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H 
       15.39        32.02         1.02        28.04        36.03        25.97 
TCGA-AG-A02X TCGA-EF-5831 TCGA-F5-6571 
       41.00         2.40        31.30 

$`2P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        37.74        10.39        14.50         8.45        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       10.39        36.03        12.00         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  2P LOSS MUTATED 2P LOSS WILD-TYPE 
             1.02              0.39 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            41.00            129.27 
  2P LOSS MUTATED 2P LOSS WILD-TYPE 
            28.04             13.97 
[1] "1.0 - 41.0 (28.0)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.4"
D43V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2P LOSS MUTATED         1        0         7         0         0         0
  2P LOSS WILD-TYPE      29        8        31         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2P LOSS MUTATED            0          1          1        1         0
  2P LOSS WILD-TYPE          9         22         13       17         9
D43V3, multiclass
            clus
vv           2P LOSS MUTATED 2P LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                7                31
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               1                22
  STAGE IIIC               1                13
  STAGE IV                 1                17
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  2P LOSS MUTATED    0  1 10  0
  2P LOSS WILD-TYPE  9 28 99 14
D43V4, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3              10                99
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2P LOSS MUTATED    8  2  1
  2P LOSS WILD-TYPE 75 43 31
D43V5, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  N0               8                75
  N1               2                43
  N2               1                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  2P LOSS MUTATED     9   1   0   1
  2P LOSS WILD-TYPE 114  21   2  12
D43V6, multiclass
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  M0                9               114
  M1                1                21
  M1A               0                 2
  MX                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                   cls
clus                 0  1
  2P LOSS MUTATED    6  5
  2P LOSS WILD-TYPE 68 83
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      6    5
  2P LOSS WILD-TYPE   68   83
        clus
vv       2P LOSS MUTATED 2P LOSS WILD-TYPE
  FEMALE               6                68
  MALE                 5                83
[1] 2 2
[1] FALSE
D43V8, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     9   1
  2P LOSS WILD-TYPE 134  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      9    1
  2P LOSS WILD-TYPE  134   12
                                clus
vv                               2P LOSS MUTATED 2P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               134
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D43V9, binary
                   cls
clus                  0   1
  2P LOSS MUTATED     1  10
  2P LOSS WILD-TYPE   5 146
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2P LOSS MUTATED      1   10
  2P LOSS WILD-TYPE    5  146
     clus
vv    2P LOSS MUTATED 2P LOSS WILD-TYPE
  NO                1                 5
  YES              10               146
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2P LOSS MUTATED     8   0   1   0
  2P LOSS WILD-TYPE 113   2  11   3
D43V10, multiclass
    clus
vv   2P LOSS MUTATED 2P LOSS WILD-TYPE
  R0               8               113
  R1               0                 2
  R2               1                11
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2P LOSS MUTATED       0                         0     3
  2P LOSS WILD-TYPE     1                         3    78
D43V12, multiclass
                           clus
vv                          2P LOSS MUTATED 2P LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   3                78
[1] 3 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     4   0
  2Q LOSS WILD-TYPE 124  22
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                4               146 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                0                22 
$`2Q LOSS MUTATED`
TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A02X TCGA-F5-6571 
       36.03        25.97        41.00        31.30 

$`2Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       17.03         0.99        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            25.97              0.39 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
            41.00            129.27 
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
           33.665            13.990 
[1] "26.0 - 41.0 (33.7)" "0.4 - 129.3 (14.0)"
[1] "hr="     "2.7e+07"
D44V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  2Q LOSS MUTATED         1        0         5         0         0         0
  2Q LOSS WILD-TYPE      29        8        33         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  2Q LOSS MUTATED            0          0          0        0         0
  2Q LOSS WILD-TYPE          9         23         14       18         9
D44V3, multiclass
            clus
vv           2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                5                33
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               0                23
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  2Q LOSS MUTATED     0   1   5   0
  2Q LOSS WILD-TYPE   9  28 104  14
D44V4, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3               5               104
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  2Q LOSS MUTATED    6  0  0
  2Q LOSS WILD-TYPE 77 45 32
D44V5, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  N0               6                77
  N1               0                45
  N2               0                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  2Q LOSS MUTATED     6   0   0   0
  2Q LOSS WILD-TYPE 117  22   2  13
D44V6, multiclass
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  M0                6               117
  M1                0                22
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                   cls
clus                 0  1
  2Q LOSS MUTATED    3  3
  2Q LOSS WILD-TYPE 71 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      3    3
  2Q LOSS WILD-TYPE   71   85
        clus
vv       2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  FEMALE               3                71
  MALE                 3                85
[1] 2 2
[1] FALSE
D44V8, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     5   0
  2Q LOSS WILD-TYPE 138  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      5    0
  2Q LOSS WILD-TYPE  138   13
                                clus
vv                               2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D44V9, binary
                   cls
clus                  0   1
  2Q LOSS MUTATED     0   6
  2Q LOSS WILD-TYPE   6 150
[1] "tbl2"
                   cls
clus                [,1] [,2]
  2Q LOSS MUTATED      0    6
  2Q LOSS WILD-TYPE    6  150
     clus
vv    2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  NO                0                 6
  YES               6               150
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  2Q LOSS MUTATED     5   0   0   0
  2Q LOSS WILD-TYPE 116   2  12   3
D44V10, multiclass
    clus
vv   2Q LOSS MUTATED 2Q LOSS WILD-TYPE
  R0               5               116
  R1               0                 2
  R2               0                12
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  2Q LOSS MUTATED       0                         0     1
  2Q LOSS WILD-TYPE     1                         3    80
D44V12, multiclass
[1] "Remove cluster labels:" "2Q LOSS MUTATED"       
clus
  2Q LOSS MUTATED 2Q LOSS WILD-TYPE 
                1                84 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AH-6544        TCGA-AH-6547 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-5917 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DC-6682        TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1DC        TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-DY-A1DG        TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6506        TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6510        TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6514        TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-6884        TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-EI-7004        TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6702 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 
       TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" "2Q LOSS WILD-TYPE" 

Clustering(45) Variable = 3P LOSS MUTATION ANALYSIS
D45V1, survival
                   sevent
clus2                 0   1
  3P LOSS MUTATED     9   3
  3P LOSS WILD-TYPE 119  19
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
               12               138 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
                3                19 
$`3P LOSS MUTATED`
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3731 TCGA-AH-6544 
       12.72        14.50         2.01        24.00         1.02         0.49 
TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6810 TCGA-G5-6233 
       10.19         6.05        13.05         5.29         0.39        18.28 

$`3P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        1.81         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30        14.86         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76         0.46        55.76        47.08        26.43 

  3P LOSS MUTATED 3P LOSS WILD-TYPE 
             0.39              0.46 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            24.00            129.27 
  3P LOSS MUTATED 3P LOSS WILD-TYPE 
            8.120            15.205 
[1] "0.4 - 24.0 (8.1)"   "0.5 - 129.3 (15.2)"
[1] "hr=" "5.7"
D45V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3P LOSS MUTATED         0        1         4         0         1         0
  3P LOSS WILD-TYPE      30        7        34         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3P LOSS MUTATED            0          2          0        5         1
  3P LOSS WILD-TYPE          9         21         14       13         8
D45V3, multiclass
            clus
vv           3P LOSS MUTATED 3P LOSS WILD-TYPE
  STAGE I                  0                30
  STAGE II                 1                 7
  STAGE IIA                4                34
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               2                21
  STAGE IIIC               0                14
  STAGE IV                 5                13
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  3P LOSS MUTATED    0  0 14  1
  3P LOSS WILD-TYPE  9 29 95 13
D45V4, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  T1               0                 9
  T2               0                29
  T3              14                95
  T4               1                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3P LOSS MUTATED    5  5  5
  3P LOSS WILD-TYPE 78 40 27
D45V5, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  N0               5                78
  N1               5                40
  N2               5                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3P LOSS MUTATED     7   6   0   1
  3P LOSS WILD-TYPE 116  16   2  12
D45V6, multiclass
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  M0                7               116
  M1                6                16
  M1A               0                 2
  MX                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                   cls
clus                 0  1
  3P LOSS MUTATED    3 12
  3P LOSS WILD-TYPE 71 76
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      3   12
  3P LOSS WILD-TYPE   71   76
        clus
vv       3P LOSS MUTATED 3P LOSS WILD-TYPE
  FEMALE               3                71
  MALE                12                76
[1] 2 2
[1] FALSE
D45V8, binary
                   cls
clus                  0   1
  3P LOSS MUTATED    10   3
  3P LOSS WILD-TYPE 133  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED     10    3
  3P LOSS WILD-TYPE  133   10
                                clus
vv                               3P LOSS MUTATED 3P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               133
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D45V9, binary
                   cls
clus                  0   1
  3P LOSS MUTATED     2  13
  3P LOSS WILD-TYPE   4 143
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3P LOSS MUTATED      2   13
  3P LOSS WILD-TYPE    4  143
     clus
vv    3P LOSS MUTATED 3P LOSS WILD-TYPE
  NO                2                 4
  YES              13               143
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3P LOSS MUTATED     7   0   4   1
  3P LOSS WILD-TYPE 114   2   8   2
D45V10, multiclass
    clus
vv   3P LOSS MUTATED 3P LOSS WILD-TYPE
  R0               7               114
  R1               0                 2
  R2               4                 8
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3P LOSS MUTATED       1                         0     8
  3P LOSS WILD-TYPE     0                         3    73
D45V12, multiclass
                           clus
vv                          3P LOSS MUTATED 3P LOSS WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   8                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(46) Variable = 3Q LOSS MUTATION ANALYSIS
D46V1, survival
                   sevent
clus2                 0   1
  3Q LOSS MUTATED     7   2
  3Q LOSS WILD-TYPE 121  20
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                9               141 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
                2                20 
$`3Q LOSS MUTATED`
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3731 TCGA-BM-6198 
       12.72        14.50        32.02         2.01         1.02        10.19 
TCGA-CI-6619 TCGA-DT-5265 TCGA-G5-6233 
        6.05         5.29        18.28 

$`3Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       36.03        12.00         8.02         7.07         1.02        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        4.60         1.81         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
             1.02              0.39 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            32.02            129.27 
  3Q LOSS MUTATED 3Q LOSS WILD-TYPE 
            10.19             15.02 
[1] "1.0 - 32.0 (10.2)"  "0.4 - 129.3 (15.0)"
[1] "hr=" "3.7"
D46V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  3Q LOSS MUTATED         0        1         2         0         1         0
  3Q LOSS WILD-TYPE      30        7        36         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  3Q LOSS MUTATED            0          1          0        4         1
  3Q LOSS WILD-TYPE          9         22         14       14         8
D46V3, multiclass
            clus
vv           3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  STAGE I                  0                30
  STAGE II                 1                 7
  STAGE IIA                2                36
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               1                22
  STAGE IIIC               0                14
  STAGE IV                 4                14
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  3Q LOSS MUTATED     0   0   9   1
  3Q LOSS WILD-TYPE   9  29 100  13
D46V4, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  T1               0                 9
  T2               0                29
  T3               9               100
  T4               1                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  3Q LOSS MUTATED    3  3  4
  3Q LOSS WILD-TYPE 80 42 28
D46V5, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  N0               3                80
  N1               3                42
  N2               4                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  3Q LOSS MUTATED     4   4   0   1
  3Q LOSS WILD-TYPE 119  18   2  12
D46V6, multiclass
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  M0                4               119
  M1                4                18
  M1A               0                 2
  MX                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                   cls
clus                 0  1
  3Q LOSS MUTATED    2  8
  3Q LOSS WILD-TYPE 72 80
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    8
  3Q LOSS WILD-TYPE   72   80
        clus
vv       3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 8                80
[1] 2 2
[1] FALSE
D46V8, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     5   4
  3Q LOSS WILD-TYPE 138   9
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      5    4
  3Q LOSS WILD-TYPE  138    9
                                clus
vv                               3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        5               138
  RECTAL MUCINOUS ADENOCARCINOMA               4                 9
[1] 2 2
[1] FALSE
D46V9, binary
                   cls
clus                  0   1
  3Q LOSS MUTATED     2   8
  3Q LOSS WILD-TYPE   4 148
[1] "tbl2"
                   cls
clus                [,1] [,2]
  3Q LOSS MUTATED      2    8
  3Q LOSS WILD-TYPE    4  148
     clus
vv    3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  NO                2                 4
  YES               8               148
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  3Q LOSS MUTATED     5   0   3   1
  3Q LOSS WILD-TYPE 116   2   9   2
D46V10, multiclass
    clus
vv   3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  R0               5               116
  R1               0                 2
  R2               3                 9
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  3Q LOSS MUTATED       1                         0     5
  3Q LOSS WILD-TYPE     0                         3    76
D46V12, multiclass
                           clus
vv                          3Q LOSS MUTATED 3Q LOSS WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   5                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(47) Variable = 4P LOSS MUTATION ANALYSIS
D47V1, survival
                   sevent
clus2                0  1
  4P LOSS MUTATED   46  5
  4P LOSS WILD-TYPE 82 17
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
               51                99 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
                5                17 
$`4P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        17.23        43.04        12.72        37.74        14.50 
TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
       15.39         1.02        34.03         6.05        19.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        32.98         1.02        35.01         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H 
       19.99        28.04        36.03        14.04        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 
       23.01        12.00        70.03        41.00         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 
        6.05         6.05         4.73        12.99        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
        7.10        30.05       126.44       129.27        32.61         2.40 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       15.85        16.34        16.41        11.97        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
        0.39         0.69        26.43 

$`4P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       17.95        13.55        19.10        10.39         8.45        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        36.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       14.01        32.02         1.02        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       38.96        61.97        38.04         0.49         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.00        13.97 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06         5.29        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       24.13        51.48         0.49        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       17.00        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        1.02         0.66         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  4P LOSS MUTATED 4P LOSS WILD-TYPE 
             0.39              0.46 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
           129.27             64.01 
  4P LOSS MUTATED 4P LOSS WILD-TYPE 
            16.34             13.05 
[1] "0.4 - 129.3 (16.3)" "0.5 - 64.0 (13.1)" 
[1] "hr=" "2"  
D47V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4P LOSS MUTATED        10        1        16         0         0         1
  4P LOSS WILD-TYPE      20        7        22         2         2         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4P LOSS MUTATED            3         11          7        5         4
  4P LOSS WILD-TYPE          6         12          7       13         5
D47V3, multiclass
            clus
vv           4P LOSS MUTATED 4P LOSS WILD-TYPE
  STAGE I                 10                20
  STAGE II                 1                 7
  STAGE IIA               16                22
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                1                 4
  STAGE IIIA               3                 6
  STAGE IIIB              11                12
  STAGE IIIC               7                 7
  STAGE IV                 5                13
  STAGE IVA                4                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4P LOSS MUTATED    2 10 43  3
  4P LOSS WILD-TYPE  7 19 66 11
D47V4, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  T1               2                 7
  T2              10                19
  T3              43                66
  T4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  4P LOSS MUTATED   27 19 12
  4P LOSS WILD-TYPE 56 26 20
D47V5, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  N0              27                56
  N1              19                26
  N2              12                20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  4P LOSS MUTATED   45  7   1  4
  4P LOSS WILD-TYPE 78 15   1  9
D47V6, multiclass
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  M0               45                78
  M1                7                15
  M1A               1                 1
  MX                4                 9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   24 34
  4P LOSS WILD-TYPE 50 54
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     24   34
  4P LOSS WILD-TYPE   50   54
        clus
vv       4P LOSS MUTATED 4P LOSS WILD-TYPE
  FEMALE              24                50
  MALE                34                54
[1] 2 2
[1] FALSE
D47V8, binary
                   cls
clus                 0  1
  4P LOSS MUTATED   53  3
  4P LOSS WILD-TYPE 90 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED     53    3
  4P LOSS WILD-TYPE   90   10
                                clus
vv                               4P LOSS MUTATED 4P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       53                90
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D47V9, binary
                   cls
clus                  0   1
  4P LOSS MUTATED     5  53
  4P LOSS WILD-TYPE   1 103
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4P LOSS MUTATED      5   53
  4P LOSS WILD-TYPE    1  103
     clus
vv    4P LOSS MUTATED 4P LOSS WILD-TYPE
  NO                5                 1
  YES              53               103
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4P LOSS MUTATED   47  0  2  0
  4P LOSS WILD-TYPE 74  2 10  3
D47V10, multiclass
    clus
vv   4P LOSS MUTATED 4P LOSS WILD-TYPE
  R0              47                74
  R1               0                 2
  R2               2                10
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4P LOSS MUTATED       0                         2    28
  4P LOSS WILD-TYPE     1                         1    53
D47V12, multiclass
                           clus
vv                          4P LOSS MUTATED 4P LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  28                53
[1] 3 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   52  5
  4Q LOSS WILD-TYPE 76 17
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
               57                93 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
                5                17 
$`4Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3600 
       37.74        14.50        15.39         1.02        34.03         6.05 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 
       19.99        29.98        32.98         1.02         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00H 
       19.99        28.04        36.03        14.04        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 
       23.01        12.00        70.03        64.01        41.00         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 
        0.69        10.19         6.05         6.05         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA 
       12.99        15.02        36.00         7.10        30.05       126.44 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
      129.27        32.61         2.40        17.00        15.85        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       16.41        11.97        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6641 
        0.66         0.69        26.43 

$`4Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       17.95        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       15.95        19.99         7.99         0.99         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       14.01        32.02         1.02        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       31.00        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        38.04         1.45         0.72         4.60         1.81 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        13.97        60.03         7.99        10.98 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        12.00        13.97        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        5.29        41.36        57.24        24.13        51.48         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       20.55        19.96        20.91        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        9.96        37.51         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
             0.39              0.46 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
           129.27             61.97 
  4Q LOSS MUTATED 4Q LOSS WILD-TYPE 
            15.85             13.05 
[1] "0.4 - 129.3 (15.8)" "0.5 - 62.0 (13.1)" 
[1] "hr=" "2.4"
D48V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  4Q LOSS MUTATED        12        2        18         0         0         2
  4Q LOSS WILD-TYPE      18        6        20         2         2         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  4Q LOSS MUTATED            3         11          8        4         4
  4Q LOSS WILD-TYPE          6         12          6       14         5
D48V3, multiclass
            clus
vv           4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  STAGE I                 12                18
  STAGE II                 2                 6
  STAGE IIA               18                20
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                2                 3
  STAGE IIIA               3                 6
  STAGE IIIB              11                12
  STAGE IIIC               8                 6
  STAGE IV                 4                14
  STAGE IVA                4                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  4Q LOSS MUTATED    2 12 47  4
  4Q LOSS WILD-TYPE  7 17 62 10
D48V4, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  T1               2                 7
  T2              12                17
  T3              47                62
  T4               4                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  4Q LOSS MUTATED   32 20 13
  4Q LOSS WILD-TYPE 51 25 19
D48V5, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  N0              32                51
  N1              20                25
  N2              13                19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  4Q LOSS MUTATED   50  7   1  6
  4Q LOSS WILD-TYPE 73 15   1  7
D48V6, multiclass
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  M0               50                73
  M1                7                15
  M1A               1                 1
  MX                6                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   26 39
  4Q LOSS WILD-TYPE 48 49
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     26   39
  4Q LOSS WILD-TYPE   48   49
        clus
vv       4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  FEMALE              26                48
  MALE                39                49
[1] 2 2
[1] FALSE
D48V8, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED   58  3
  4Q LOSS WILD-TYPE 85 10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED     58    3
  4Q LOSS WILD-TYPE   85   10
                                clus
vv                               4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       58                85
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D48V9, binary
                   cls
clus                 0  1
  4Q LOSS MUTATED    5 60
  4Q LOSS WILD-TYPE  1 96
[1] "tbl2"
                   cls
clus                [,1] [,2]
  4Q LOSS MUTATED      5   60
  4Q LOSS WILD-TYPE    1   96
     clus
vv    4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  NO                5                 1
  YES              60                96
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  4Q LOSS MUTATED   50  0  2  0
  4Q LOSS WILD-TYPE 71  2 10  3
D48V10, multiclass
    clus
vv   4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  R0              50                71
  R1               0                 2
  R2               2                10
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  4Q LOSS MUTATED       0                         2    36
  4Q LOSS WILD-TYPE     1                         1    45
D48V12, multiclass
                           clus
vv                          4Q LOSS MUTATED 4Q LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               2                 1
  WHITE                                  36                45
[1] 3 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    19   2
  5P LOSS WILD-TYPE 109  20
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
               21               129 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
                2                20 
$`5P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-6136 TCGA-AG-3600 TCGA-AG-3731 TCGA-AG-3882 
       24.13        43.04        15.39         6.05         1.02        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A01W TCGA-CI-6620 
        1.02        48.03        28.04        23.01        70.03         6.05 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-EI-6506 TCGA-EI-6881 
       13.97        36.00       126.44        57.24        20.55        16.41 
TCGA-EI-6885 TCGA-EI-7004 TCGA-G5-6233 
       13.64         8.45        18.28 

$`5P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39        14.50         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99        29.98        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
       36.95        17.03        13.02        35.01        14.01        32.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        31.00        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81        10.19         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        12.00        15.02         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE 
       12.95        13.05        10.06         5.29        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       24.13        51.48        32.61         0.49         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 
       16.31         8.61        11.51        10.78        17.46        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  5P LOSS MUTATED 5P LOSS WILD-TYPE 
             1.02              0.39 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
           126.44            129.27 
  5P LOSS MUTATED 5P LOSS WILD-TYPE 
            19.99             13.94 
[1] "1.0 - 126.4 (20.0)" "0.4 - 129.3 (13.9)"
[1] "hr=" "2.8"
D49V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5P LOSS MUTATED         4        1         6         0         1         2
  5P LOSS WILD-TYPE      26        7        32         2         1         3
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5P LOSS MUTATED            2          2          3        3         2
  5P LOSS WILD-TYPE          7         21         11       15         7
D49V3, multiclass
            clus
vv           5P LOSS MUTATED 5P LOSS WILD-TYPE
  STAGE I                  4                26
  STAGE II                 1                 7
  STAGE IIA                6                32
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                2                 3
  STAGE IIIA               2                 7
  STAGE IIIB               2                21
  STAGE IIIC               3                11
  STAGE IV                 3                15
  STAGE IVA                2                 7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5P LOSS MUTATED    1  4 20  1
  5P LOSS WILD-TYPE  8 25 89 13
D49V4, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  T1               1                 8
  T2               4                25
  T3              20                89
  T4               1                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5P LOSS MUTATED   11  8  7
  5P LOSS WILD-TYPE 72 37 25
D49V5, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  N0              11                72
  N1               8                37
  N2               7                25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  5P LOSS MUTATED    20   4   0   2
  5P LOSS WILD-TYPE 103  18   2  11
D49V6, multiclass
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  M0               20               103
  M1                4                18
  M1A               0                 2
  MX                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                   cls
clus                 0  1
  5P LOSS MUTATED   16 10
  5P LOSS WILD-TYPE 58 78
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     16   10
  5P LOSS WILD-TYPE   58   78
        clus
vv       5P LOSS MUTATED 5P LOSS WILD-TYPE
  FEMALE              16                58
  MALE                10                78
[1] 2 2
[1] FALSE
D49V8, binary
                   cls
clus                  0   1
  5P LOSS MUTATED    25   1
  5P LOSS WILD-TYPE 118  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED     25    1
  5P LOSS WILD-TYPE  118   12
                                clus
vv                               5P LOSS MUTATED 5P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       25               118
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D49V9, binary
                   cls
clus                  0   1
  5P LOSS MUTATED     2  24
  5P LOSS WILD-TYPE   4 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5P LOSS MUTATED      2   24
  5P LOSS WILD-TYPE    4  132
     clus
vv    5P LOSS MUTATED 5P LOSS WILD-TYPE
  NO                2                 4
  YES              24               132
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  5P LOSS MUTATED    19   0   2   0
  5P LOSS WILD-TYPE 102   2  10   3
D49V10, multiclass
    clus
vv   5P LOSS MUTATED 5P LOSS WILD-TYPE
  R0              19               102
  R1               0                 2
  R2               2                10
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5P LOSS MUTATED       0                         1    13
  5P LOSS WILD-TYPE     1                         2    68
D49V12, multiclass
                           clus
vv                          5P LOSS MUTATED 5P LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                  13                68
[1] 3 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    27   8
  5Q LOSS WILD-TYPE 101  14
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
               35               115 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
                8                14 
$`5Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6672 
       24.13        17.23        43.04        37.74        15.39        10.39 
TCGA-AG-3578 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3896 
       32.02        29.98         1.02        32.98        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y TCGA-AG-A01W 
       48.03        28.04        36.03        17.03        23.01        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 
       64.01         1.94        38.96        10.19         6.05        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        36.00         7.10        13.05       126.44        57.24 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6881 TCGA-F5-6702 TCGA-G5-6233 
       51.48        20.55        16.41        14.86        18.28 

$`5Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       17.95        13.55        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
        8.45        20.02        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       19.99        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        12.00        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 
        0.69         0.72         4.60         1.81         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        12.99        12.00        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
       10.06         5.29        41.36       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
             1.02              0.39 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
           126.44            129.27 
  5Q LOSS MUTATED 5Q LOSS WILD-TYPE 
            20.55             12.95 
[1] "1.0 - 126.4 (20.6)" "0.4 - 129.3 (12.9)"
[1] "hr=" "1"  
D50V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  5Q LOSS MUTATED         6        3        11         0         1         1
  5Q LOSS WILD-TYPE      24        5        27         2         1         4
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  5Q LOSS MUTATED            2          4          4        4         4
  5Q LOSS WILD-TYPE          7         19         10       14         5
D50V3, multiclass
            clus
vv           5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 3                 5
  STAGE IIA               11                27
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                1                 4
  STAGE IIIA               2                 7
  STAGE IIIB               4                19
  STAGE IIIC               4                10
  STAGE IV                 4                14
  STAGE IVA                4                 5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  5Q LOSS MUTATED    1  7 29  3
  5Q LOSS WILD-TYPE  8 22 80 11
D50V4, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  T1               1                 8
  T2               7                22
  T3              29                80
  T4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  5Q LOSS MUTATED   20 11  9
  5Q LOSS WILD-TYPE 63 34 23
D50V5, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  N0              20                63
  N1              11                34
  N2               9                23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  5Q LOSS MUTATED   29  6   1  3
  5Q LOSS WILD-TYPE 94 16   1 10
D50V6, multiclass
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  M0               29                94
  M1                6                16
  M1A               1                 1
  MX                3                10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                   cls
clus                 0  1
  5Q LOSS MUTATED   20 20
  5Q LOSS WILD-TYPE 54 68
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     20   20
  5Q LOSS WILD-TYPE   54   68
        clus
vv       5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  FEMALE              20                54
  MALE                20                68
[1] 2 2
[1] FALSE
D50V8, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED    38   1
  5Q LOSS WILD-TYPE 105  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED     38    1
  5Q LOSS WILD-TYPE  105   12
                                clus
vv                               5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       38               105
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D50V9, binary
                   cls
clus                  0   1
  5Q LOSS MUTATED     5  35
  5Q LOSS WILD-TYPE   1 121
[1] "tbl2"
                   cls
clus                [,1] [,2]
  5Q LOSS MUTATED      5   35
  5Q LOSS WILD-TYPE    1  121
     clus
vv    5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  NO                5                 1
  YES              35               121
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  5Q LOSS MUTATED   28  1  3  0
  5Q LOSS WILD-TYPE 93  1  9  3
D50V10, multiclass
    clus
vv   5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  R0              28                93
  R1               1                 1
  R2               3                 9
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  5Q LOSS MUTATED       0                         1    19
  5Q LOSS WILD-TYPE     1                         2    62
D50V12, multiclass
                           clus
vv                          5Q LOSS MUTATED 5Q LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                  19                62
[1] 3 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     8   3
  6P LOSS WILD-TYPE 120  19
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
               11               139 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
                3                19 
$`6P LOSS MUTATED`
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-A008 
       17.23        13.55        12.72        24.00        34.03        13.94 
TCGA-AG-A011 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6883 
       37.02        13.05         5.29        24.13        11.51 

$`6P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02        17.03         0.99        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  6P LOSS MUTATED 6P LOSS WILD-TYPE 
             5.29              0.39 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            37.02            129.27 
  6P LOSS MUTATED 6P LOSS WILD-TYPE 
            13.94             14.50 
[1] "5.3 - 37.0 (13.9)"  "0.4 - 129.3 (14.5)"
[1] "hr=" "2.7"
D51V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6P LOSS MUTATED         1        1         7         0         1         0
  6P LOSS WILD-TYPE      29        7        31         2         1         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6P LOSS MUTATED            0          0          2        1         0
  6P LOSS WILD-TYPE          9         23         12       17         9
D51V3, multiclass
            clus
vv           6P LOSS MUTATED 6P LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 1                 7
  STAGE IIA                7                31
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               0                23
  STAGE IIIC               2                12
  STAGE IV                 1                17
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6P LOSS MUTATED    0  1 12  0
  6P LOSS WILD-TYPE  9 28 97 14
D51V4, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3              12                97
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6P LOSS MUTATED   10  0  3
  6P LOSS WILD-TYPE 73 45 29
D51V5, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  N0              10                73
  N1               0                45
  N2               3                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6P LOSS MUTATED    12   1   0   0
  6P LOSS WILD-TYPE 111  21   2  13
D51V6, multiclass
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  M0               12               111
  M1                1                21
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                   cls
clus                 0  1
  6P LOSS MUTATED    6  7
  6P LOSS WILD-TYPE 68 81
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      6    7
  6P LOSS WILD-TYPE   68   81
        clus
vv       6P LOSS MUTATED 6P LOSS WILD-TYPE
  FEMALE               6                68
  MALE                 7                81
[1] 2 2
[1] FALSE
D51V8, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     9   3
  6P LOSS WILD-TYPE 134  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      9    3
  6P LOSS WILD-TYPE  134   10
                                clus
vv                               6P LOSS MUTATED 6P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        9               134
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D51V9, binary
                   cls
clus                  0   1
  6P LOSS MUTATED     1  12
  6P LOSS WILD-TYPE   5 144
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6P LOSS MUTATED      1   12
  6P LOSS WILD-TYPE    5  144
     clus
vv    6P LOSS MUTATED 6P LOSS WILD-TYPE
  NO                1                 5
  YES              12               144
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6P LOSS MUTATED    10   0   1   1
  6P LOSS WILD-TYPE 111   2  11   2
D51V10, multiclass
    clus
vv   6P LOSS MUTATED 6P LOSS WILD-TYPE
  R0              10               111
  R1               0                 2
  R2               1                11
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6P LOSS MUTATED       1                         0     6
  6P LOSS WILD-TYPE     0                         3    75
D51V12, multiclass
                           clus
vv                          6P LOSS MUTATED 6P LOSS WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   6                75
[1] 3 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    16   3
  6Q LOSS WILD-TYPE 112  19
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
               19               131 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
                3                19 
$`6Q LOSS MUTATED`
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 
       17.23        13.55        19.10        12.72        12.00        32.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-4005 TCGA-AG-A008 
       24.00        46.03        34.03         6.05        14.04        13.94 
TCGA-AG-A011 TCGA-AH-6544 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6883 TCGA-G5-6233 
       37.02         0.49        13.05         5.29        11.51        18.28 
TCGA-G5-6641 
       26.43 

$`6Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       24.13        17.95        43.04        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 
        8.45        15.39        20.02        10.39        36.03         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        7.07         1.02         2.01         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03         1.02        17.03         0.99        20.98         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       12.95        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        55.76        47.08 

  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
             0.49              0.39 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            46.03            129.27 
  6Q LOSS MUTATED 6Q LOSS WILD-TYPE 
            14.04             14.50 
[1] "0.5 - 46.0 (14.0)"  "0.4 - 129.3 (14.5)"
[1] "hr=" "1.4"
D52V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  6Q LOSS MUTATED         3        2         8         0         2         0
  6Q LOSS WILD-TYPE      27        6        30         2         0         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  6Q LOSS MUTATED            1          0          3        2         0
  6Q LOSS WILD-TYPE          8         23         11       16         9
D52V3, multiclass
            clus
vv           6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  STAGE I                  3                27
  STAGE II                 2                 6
  STAGE IIA                8                30
  STAGE IIB                0                 2
  STAGE IIC                2                 0
  STAGE III                0                 5
  STAGE IIIA               1                 8
  STAGE IIIB               0                23
  STAGE IIIC               3                11
  STAGE IV                 2                16
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  6Q LOSS MUTATED    1  3 18  0
  6Q LOSS WILD-TYPE  8 26 91 14
D52V4, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  T1               1                 8
  T2               3                26
  T3              18                91
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  6Q LOSS MUTATED   14  2  6
  6Q LOSS WILD-TYPE 69 43 26
D52V5, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  N0              14                69
  N1               2                43
  N2               6                26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  6Q LOSS MUTATED    17   3   0   2
  6Q LOSS WILD-TYPE 106  19   2  11
D52V6, multiclass
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  M0               17               106
  M1                3                19
  M1A               0                 2
  MX                2                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                   cls
clus                 0  1
  6Q LOSS MUTATED    7 15
  6Q LOSS WILD-TYPE 67 73
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      7   15
  6Q LOSS WILD-TYPE   67   73
        clus
vv       6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  FEMALE               7                67
  MALE                15                73
[1] 2 2
[1] FALSE
D52V8, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED    15   5
  6Q LOSS WILD-TYPE 128   8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED     15    5
  6Q LOSS WILD-TYPE  128    8
                                clus
vv                               6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       15               128
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 2 2
[1] FALSE
D52V9, binary
                   cls
clus                  0   1
  6Q LOSS MUTATED     1  21
  6Q LOSS WILD-TYPE   5 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  6Q LOSS MUTATED      1   21
  6Q LOSS WILD-TYPE    5  135
     clus
vv    6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  NO                1                 5
  YES              21               135
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  6Q LOSS MUTATED    18   0   1   1
  6Q LOSS WILD-TYPE 103   2  11   2
D52V10, multiclass
    clus
vv   6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  R0              18               103
  R1               0                 2
  R2               1                11
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  6Q LOSS MUTATED       1                         0     9
  6Q LOSS WILD-TYPE     0                         3    72
D52V12, multiclass
                           clus
vv                          6Q LOSS MUTATED 6Q LOSS WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   9                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(53) Variable = 7Q LOSS MUTATION ANALYSIS
D53V1, survival
                   sevent
clus2                 0   1
  7Q LOSS MUTATED     2   0
  7Q LOSS WILD-TYPE 126  22
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                2               148 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                0                22 
$`7Q LOSS MUTATED`
TCGA-AG-A008 TCGA-DC-6682 
       13.94        13.05 

$`7Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.05              0.39 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
            13.94            129.27 
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
           13.495            14.680 
[1] "13.1 - 13.9 (13.5)" "0.4 - 129.3 (14.7)"
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
D53V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  7Q LOSS MUTATED         1        0         2         0         0         0
  7Q LOSS WILD-TYPE      29        8        36         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  7Q LOSS MUTATED            0          0          0        0         0
  7Q LOSS WILD-TYPE          9         23         14       18         9
D53V3, multiclass
            clus
vv           7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  STAGE I                  1                29
  STAGE II                 0                 8
  STAGE IIA                2                36
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               0                23
  STAGE IIIC               0                14
  STAGE IV                 0                18
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  7Q LOSS MUTATED     0   1   2   0
  7Q LOSS WILD-TYPE   9  28 107  14
D53V4, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  T1               0                 9
  T2               1                28
  T3               2               107
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  7Q LOSS MUTATED    3  0  0
  7Q LOSS WILD-TYPE 80 45 32
D53V5, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  N0               3                80
  N1               0                45
  N2               0                32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  7Q LOSS MUTATED     3   0   0   0
  7Q LOSS WILD-TYPE 120  22   2  13
D53V6, multiclass
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  M0                3               120
  M1                0                22
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                   cls
clus                 0  1
  7Q LOSS MUTATED    2  1
  7Q LOSS WILD-TYPE 72 87
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE   72   87
        clus
vv       7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 1                87
[1] 2 2
[1] FALSE
D53V8, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     2   1
  7Q LOSS WILD-TYPE 141  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      2    1
  7Q LOSS WILD-TYPE  141   12
                                clus
vv                               7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        2               141
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D53V9, binary
                   cls
clus                  0   1
  7Q LOSS MUTATED     0   3
  7Q LOSS WILD-TYPE   6 153
[1] "tbl2"
                   cls
clus                [,1] [,2]
  7Q LOSS MUTATED      0    3
  7Q LOSS WILD-TYPE    6  153
     clus
vv    7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  NO                0                 6
  YES               3               153
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  7Q LOSS MUTATED     3   0   0   0
  7Q LOSS WILD-TYPE 118   2  12   3
D53V10, multiclass
    clus
vv   7Q LOSS MUTATED 7Q LOSS WILD-TYPE
  R0               3               118
  R1               0                 2
  R2               0                12
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  7Q LOSS MUTATED       0                         0     1
  7Q LOSS WILD-TYPE     1                         3    80
D53V12, multiclass
[1] "Remove cluster labels:" "7Q LOSS MUTATED"       
clus
  7Q LOSS MUTATED 7Q LOSS WILD-TYPE 
                1                84 
       TCGA-AF-2687        TCGA-AF-2689        TCGA-AF-2690        TCGA-AF-2691 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-2692        TCGA-AF-2693        TCGA-AF-3400        TCGA-AF-3911 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-3913        TCGA-AF-4110        TCGA-AF-5654        TCGA-AF-6136 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AF-6655        TCGA-AF-6672        TCGA-AH-6544        TCGA-AH-6547 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-AH-6643        TCGA-AH-6644        TCGA-AH-6897        TCGA-AH-6903 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-BM-6198        TCGA-CI-6619        TCGA-CI-6620        TCGA-CI-6621 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CI-6622        TCGA-CI-6623        TCGA-CI-6624        TCGA-CL-5917 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-CL-5918        TCGA-DC-4745        TCGA-DC-4749        TCGA-DC-5337 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DC-5869        TCGA-DC-6154        TCGA-DC-6155        TCGA-DC-6156 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DC-6157        TCGA-DC-6158        TCGA-DC-6160        TCGA-DC-6681 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DC-6683        TCGA-DT-5265        TCGA-DY-A0XA        TCGA-DY-A1DC 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DY-A1DD        TCGA-DY-A1DE        TCGA-DY-A1DF        TCGA-DY-A1DG 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-DY-A1H8        TCGA-EF-5830        TCGA-EF-5831        TCGA-EI-6506 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6507        TCGA-EI-6508        TCGA-EI-6509        TCGA-EI-6510 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6511        TCGA-EI-6512        TCGA-EI-6513        TCGA-EI-6514 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6881        TCGA-EI-6882        TCGA-EI-6883        TCGA-EI-6884 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-EI-6885        TCGA-EI-6917        TCGA-EI-7002        TCGA-EI-7004 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F5-6464        TCGA-F5-6465        TCGA-F5-6571        TCGA-F5-6702 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F5-6810        TCGA-F5-6811        TCGA-F5-6812        TCGA-F5-6813 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-F5-6814        TCGA-F5-6861        TCGA-F5-6863        TCGA-F5-6864 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 
       TCGA-G5-6233        TCGA-G5-6235        TCGA-G5-6572        TCGA-G5-6641 
"7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" "7Q LOSS WILD-TYPE" 

Clustering(54) Variable = 8P LOSS MUTATION ANALYSIS
D54V1, survival
                   sevent
clus2                0  1
  8P LOSS MUTATED   56 14
  8P LOSS WILD-TYPE 72  8
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               70                80 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
               14                 8 
$`8P LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       17.95        17.23        43.04        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       10.39        15.39        10.39         1.02        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 
       46.03        34.03         2.01         6.05         0.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 
        0.99        29.98        32.98         0.99         1.02        17.03 
TCGA-AG-3893 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       35.01        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02        15.95         1.02        12.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98         1.94        38.96        41.00         1.45 
TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       10.19         4.73        13.97        60.03        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6683 TCGA-DT-5265 
       12.99        13.97        36.00         7.10        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 
      126.44       129.27        51.48         2.40        15.85        16.34 
TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       10.78        11.97         8.45         9.96        31.30        14.86 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.69         0.46        18.28        26.43 

$`8P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 
       24.13        12.72        14.50         8.45        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 
       12.00        32.02         8.02         7.07         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3878 
       12.03        15.95        19.99        19.99         1.02         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       19.99        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       32.02         1.02         0.99        20.98        13.94         6.02 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A025 
       36.03         9.07        31.00        70.03        64.01        49.97 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       61.97        38.04         0.49         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 
        1.81         6.05         6.05         6.97         9.37         7.99 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        12.00        15.02        30.05        12.95        13.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        32.61         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 
       16.41         8.61        11.51        13.64        17.46        37.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         1.02         0.66         0.53         1.12         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  8P LOSS MUTATED 8P LOSS WILD-TYPE 
             0.46              0.39 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           129.27             70.03 
  8P LOSS MUTATED 8P LOSS WILD-TYPE 
           14.450            14.255 
[1] "0.5 - 129.3 (14.4)" "0.4 - 70.0 (14.3)" 
[1] "hr=" "2"  
D54V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8P LOSS MUTATED        14        2        17         0         1         3
  8P LOSS WILD-TYPE      16        6        21         2         1         2
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8P LOSS MUTATED            4         12          8       10         3
  8P LOSS WILD-TYPE          5         11          6        8         6
D54V3, multiclass
            clus
vv           8P LOSS MUTATED 8P LOSS WILD-TYPE
  STAGE I                 14                16
  STAGE II                 2                 6
  STAGE IIA               17                21
  STAGE IIB                0                 2
  STAGE IIC                1                 1
  STAGE III                3                 2
  STAGE IIIA               4                 5
  STAGE IIIB              12                11
  STAGE IIIC               8                 6
  STAGE IV                10                 8
  STAGE IVA                3                 6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  8P LOSS MUTATED    3 14 51  7
  8P LOSS WILD-TYPE  6 15 58  7
D54V4, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  T1               3                 6
  T2              14                15
  T3              51                58
  T4               7                 7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  8P LOSS MUTATED   34 24 17
  8P LOSS WILD-TYPE 49 21 15
D54V5, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  N0              34                49
  N1              24                21
  N2              17                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                M0 M1 M1A MX
  8P LOSS MUTATED   56 11   0  7
  8P LOSS WILD-TYPE 67 11   2  6
D54V6, multiclass
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  M0               56                67
  M1               11                11
  M1A               0                 2
  MX                7                 6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   33 42
  8P LOSS WILD-TYPE 41 46
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     33   42
  8P LOSS WILD-TYPE   41   46
        clus
vv       8P LOSS MUTATED 8P LOSS WILD-TYPE
  FEMALE              33                41
  MALE                42                46
[1] 2 2
[1] FALSE
D54V8, binary
                   cls
clus                 0  1
  8P LOSS MUTATED   67  5
  8P LOSS WILD-TYPE 76  8
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED     67    5
  8P LOSS WILD-TYPE   76    8
                                clus
vv                               8P LOSS MUTATED 8P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       67                76
  RECTAL MUCINOUS ADENOCARCINOMA               5                 8
[1] 2 2
[1] FALSE
D54V9, binary
                   cls
clus                 0  1
  8P LOSS MUTATED    4 71
  8P LOSS WILD-TYPE  2 85
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8P LOSS MUTATED      4   71
  8P LOSS WILD-TYPE    2   85
     clus
vv    8P LOSS MUTATED 8P LOSS WILD-TYPE
  NO                4                 2
  YES              71                85
[1] 2 2
[1] FALSE
                   vv
clus                R0 R1 R2 RX
  8P LOSS MUTATED   56  1  6  2
  8P LOSS WILD-TYPE 65  1  6  1
D54V10, multiclass
    clus
vv   8P LOSS MUTATED 8P LOSS WILD-TYPE
  R0              56                65
  R1               1                 1
  R2               6                 6
  RX               2                 1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8P LOSS MUTATED       1                         3    33
  8P LOSS WILD-TYPE     0                         0    48
D54V12, multiclass
                           clus
vv                          8P LOSS MUTATED 8P LOSS WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               3                 0
  WHITE                                  33                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(55) Variable = 8Q LOSS MUTATION ANALYSIS
D55V1, survival
                   sevent
clus2                 0   1
  8Q LOSS MUTATED     9   1
  8Q LOSS WILD-TYPE 119  21
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
               10               140 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
                1                21 
$`8Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AG-3605 TCGA-AG-3883 TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A02X 
       13.55         0.99         1.02        23.01        12.00        41.00 
TCGA-DC-6157 TCGA-DY-A1DG TCGA-EI-6511 TCGA-F5-6813 
       36.00        51.48        15.85         0.69 

$`8Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 
       20.98        13.94         6.02        25.97        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
       15.02        12.99        12.00        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       30.05        12.95        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
             0.69              0.39 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            51.48            129.27 
  8Q LOSS MUTATED 8Q LOSS WILD-TYPE 
            14.70             14.27 
[1] "0.7 - 51.5 (14.7)"  "0.4 - 129.3 (14.3)"
[1] "hr=" "1.4"
D55V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  8Q LOSS MUTATED         3        0         3         0         0         0
  8Q LOSS WILD-TYPE      27        8        35         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  8Q LOSS MUTATED            0          2          1        1         1
  8Q LOSS WILD-TYPE          9         21         13       17         8
D55V3, multiclass
            clus
vv           8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  STAGE I                  3                27
  STAGE II                 0                 8
  STAGE IIA                3                35
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               0                 9
  STAGE IIIB               2                21
  STAGE IIIC               1                13
  STAGE IV                 1                17
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 T1  T2  T3  T4
  8Q LOSS MUTATED     0   3   7   1
  8Q LOSS WILD-TYPE   9  26 102  13
D55V4, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  T1               0                 9
  T2               3                26
  T3               7               102
  T4               1                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  8Q LOSS MUTATED    6  4  1
  8Q LOSS WILD-TYPE 77 41 31
D55V5, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  N0               6                77
  N1               4                41
  N2               1                31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  8Q LOSS MUTATED     9   2   0   0
  8Q LOSS WILD-TYPE 114  20   2  13
D55V6, multiclass
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  M0                9               114
  M1                2                20
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                   cls
clus                 0  1
  8Q LOSS MUTATED    2  9
  8Q LOSS WILD-TYPE 72 79
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      2    9
  8Q LOSS WILD-TYPE   72   79
        clus
vv       8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  FEMALE               2                72
  MALE                 9                79
[1] 2 2
[1] FALSE
D55V8, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED    10   0
  8Q LOSS WILD-TYPE 133  13
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED     10    0
  8Q LOSS WILD-TYPE  133   13
                                clus
vv                               8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       10               133
  RECTAL MUCINOUS ADENOCARCINOMA               0                13
[1] 2 2
[1] FALSE
D55V9, binary
                   cls
clus                  0   1
  8Q LOSS MUTATED     0  11
  8Q LOSS WILD-TYPE   6 145
[1] "tbl2"
                   cls
clus                [,1] [,2]
  8Q LOSS MUTATED      0   11
  8Q LOSS WILD-TYPE    6  145
     clus
vv    8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  NO                0                 6
  YES              11               145
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  8Q LOSS MUTATED     9   0   1   0
  8Q LOSS WILD-TYPE 112   2  11   3
D55V10, multiclass
    clus
vv   8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  R0               9               112
  R1               0                 2
  R2               1                11
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  8Q LOSS MUTATED       0                         1     4
  8Q LOSS WILD-TYPE     1                         2    77
D55V12, multiclass
                           clus
vv                          8Q LOSS MUTATED 8Q LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               1                 2
  WHITE                                   4                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(56) Variable = 9P LOSS MUTATION ANALYSIS
D56V1, survival
                   sevent
clus2                 0   1
  9P LOSS MUTATED    16   5
  9P LOSS WILD-TYPE 112  17
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
               21               129 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
                5                17 
$`9P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3731 
       24.13        13.55         2.01        34.03         6.05         1.02 
TCGA-AG-3882 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G 
       19.99        15.95        12.00        31.00         1.94        38.96 
TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 
        6.05         4.73        13.97        11.01         7.10        30.05 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6514 
       51.48         0.49        16.31 

$`9P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        43.04        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W 
       23.01        37.02        36.03         9.07         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
        1.81        10.19         6.05         6.97         9.37        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        36.00        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  9P LOSS MUTATED 9P LOSS WILD-TYPE 
             0.49              0.39 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            51.48            129.27 
  9P LOSS MUTATED 9P LOSS WILD-TYPE 
            13.55             14.86 
[1] "0.5 - 51.5 (13.6)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "2.5"
D56V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9P LOSS MUTATED         6        1         3         1         0         0
  9P LOSS WILD-TYPE      24        7        35         1         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9P LOSS MUTATED            1          1          2        6         1
  9P LOSS WILD-TYPE          8         22         12       12         8
D56V3, multiclass
            clus
vv           9P LOSS MUTATED 9P LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA                3                35
  STAGE IIB                1                 1
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               1                 8
  STAGE IIIB               1                22
  STAGE IIIC               2                12
  STAGE IV                 6                12
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9P LOSS MUTATED    0  8 12  2
  9P LOSS WILD-TYPE  9 21 97 12
D56V4, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  T1               0                 9
  T2               8                21
  T3              12                97
  T4               2                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9P LOSS MUTATED   12  6  4
  9P LOSS WILD-TYPE 71 39 28
D56V5, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  N0              12                71
  N1               6                39
  N2               4                28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  9P LOSS MUTATED    15   7   0   0
  9P LOSS WILD-TYPE 108  15   2  13
D56V6, multiclass
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  M0               15               108
  M1                7                15
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                   cls
clus                 0  1
  9P LOSS MUTATED    8 14
  9P LOSS WILD-TYPE 66 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      8   14
  9P LOSS WILD-TYPE   66   74
        clus
vv       9P LOSS MUTATED 9P LOSS WILD-TYPE
  FEMALE               8                66
  MALE                14                74
[1] 2 2
[1] FALSE
D56V8, binary
                   cls
clus                  0   1
  9P LOSS MUTATED    20   1
  9P LOSS WILD-TYPE 123  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED     20    1
  9P LOSS WILD-TYPE  123   12
                                clus
vv                               9P LOSS MUTATED 9P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       20               123
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D56V9, binary
                   cls
clus                  0   1
  9P LOSS MUTATED     1  21
  9P LOSS WILD-TYPE   5 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9P LOSS MUTATED      1   21
  9P LOSS WILD-TYPE    5  135
     clus
vv    9P LOSS MUTATED 9P LOSS WILD-TYPE
  NO                1                 5
  YES              21               135
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9P LOSS MUTATED    12   1   5   0
  9P LOSS WILD-TYPE 109   1   7   3
D56V10, multiclass
    clus
vv   9P LOSS MUTATED 9P LOSS WILD-TYPE
  R0              12               109
  R1               1                 1
  R2               5                 7
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9P LOSS MUTATED       0                         0    10
  9P LOSS WILD-TYPE     1                         3    71
D56V12, multiclass
                           clus
vv                          9P LOSS MUTATED 9P LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                  10                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(57) Variable = 9Q LOSS MUTATION ANALYSIS
D57V1, survival
                   sevent
clus2                 0   1
  9Q LOSS MUTATED    16   5
  9Q LOSS WILD-TYPE 112  17
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
               21               129 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
                5                17 
$`9Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3731 TCGA-AG-3882 
       24.13        13.55         2.01        34.03         1.02        19.99 
TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A02G 
       36.03        15.95        12.00        31.00         1.94        38.96 
TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-6158 TCGA-DC-6160 
        6.05         4.73        13.97        11.01         7.10        30.05 
TCGA-EF-5830 TCGA-EI-6514 TCGA-F5-6702 
        0.49        16.31        14.86 

$`9Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.95        17.23        43.04        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99        29.98        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W 
       23.01        37.02        36.03         9.07         1.02        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       64.01        10.98        51.98        49.97        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
        1.81        10.19         6.05         6.97         9.37        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        36.00        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
             0.49              0.39 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            38.96            129.27 
  9Q LOSS MUTATED 9Q LOSS WILD-TYPE 
            13.97             14.50 
[1] "0.5 - 39.0 (14.0)"  "0.4 - 129.3 (14.5)"
[1] "hr=" "2.9"
D57V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  9Q LOSS MUTATED         6        1         4         1         0         0
  9Q LOSS WILD-TYPE      24        7        34         1         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  9Q LOSS MUTATED            1          2          1        5         1
  9Q LOSS WILD-TYPE          8         21         13       13         8
D57V3, multiclass
            clus
vv           9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  STAGE I                  6                24
  STAGE II                 1                 7
  STAGE IIA                4                34
  STAGE IIB                1                 1
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               1                 8
  STAGE IIIB               2                21
  STAGE IIIC               1                13
  STAGE IV                 5                13
  STAGE IVA                1                 8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  9Q LOSS MUTATED    0  8 11  3
  9Q LOSS WILD-TYPE  9 21 98 11
D57V4, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  T1               0                 9
  T2               8                21
  T3              11                98
  T4               3                11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  9Q LOSS MUTATED   13  7  2
  9Q LOSS WILD-TYPE 70 38 30
D57V5, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  N0              13                70
  N1               7                38
  N2               2                30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  9Q LOSS MUTATED    16   6   0   0
  9Q LOSS WILD-TYPE 107  16   2  13
D57V6, multiclass
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  M0               16               107
  M1                6                16
  M1A               0                 2
  MX                0                13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                   cls
clus                 0  1
  9Q LOSS MUTATED    8 14
  9Q LOSS WILD-TYPE 66 74
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      8   14
  9Q LOSS WILD-TYPE   66   74
        clus
vv       9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  FEMALE               8                66
  MALE                14                74
[1] 2 2
[1] FALSE
D57V8, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED    20   1
  9Q LOSS WILD-TYPE 123  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED     20    1
  9Q LOSS WILD-TYPE  123   12
                                clus
vv                               9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       20               123
  RECTAL MUCINOUS ADENOCARCINOMA               1                12
[1] 2 2
[1] FALSE
D57V9, binary
                   cls
clus                  0   1
  9Q LOSS MUTATED     1  21
  9Q LOSS WILD-TYPE   5 135
[1] "tbl2"
                   cls
clus                [,1] [,2]
  9Q LOSS MUTATED      1   21
  9Q LOSS WILD-TYPE    5  135
     clus
vv    9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  NO                1                 5
  YES              21               135
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  9Q LOSS MUTATED    13   1   5   0
  9Q LOSS WILD-TYPE 108   1   7   3
D57V10, multiclass
    clus
vv   9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  R0              13               108
  R1               1                 1
  R2               5                 7
  RX               0                 3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  9Q LOSS MUTATED       0                         0    10
  9Q LOSS WILD-TYPE     1                         3    71
D57V12, multiclass
                           clus
vv                          9Q LOSS MUTATED 9Q LOSS WILD-TYPE
  ASIAN                                   0                 1
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                  10                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(58) Variable = 10P LOSS MUTATION ANALYSIS
D58V1, survival
                    sevent
clus2                 0  1
  10P LOSS MUTATED   30  1
  10P LOSS WILD-TYPE 98 21
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                31                119 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
                 1                 21 
$`10P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3587 TCGA-AG-3593 
       24.13        13.55        12.72        10.39        46.03        34.03 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A01L 
       36.95         1.02        19.99        13.94        25.97        12.00 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6156 
       10.98        41.00         0.49         4.73        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6509 
       36.00        13.05        10.06       129.27         0.49        17.00 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6864 
       16.34        16.31        16.41         8.45        14.86         0.46 
TCGA-G5-6641 
       26.43 

$`10P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        15.39        20.02        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.05         6.97         9.37        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6158 
       10.98        11.01        15.02        12.99        12.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95         5.29       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        15.85        17.69         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       31.30         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        18.28        55.76        47.08 

  10P LOSS MUTATED 10P LOSS WILD-TYPE 
              0.46               0.39 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
            129.27             126.44 
  10P LOSS MUTATED 10P LOSS WILD-TYPE 
             14.86              14.04 
[1] "0.5 - 129.3 (14.9)" "0.4 - 126.4 (14.0)"
[1] "hr=" "4.7"
D58V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10P LOSS MUTATED         6        0         9         1         0         1
  10P LOSS WILD-TYPE      24        8        29         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10P LOSS MUTATED            3          4          3        1         3
  10P LOSS WILD-TYPE          6         19         11       17         6
D58V3, multiclass
            clus
vv           10P LOSS MUTATED 10P LOSS WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  0                  8
  STAGE IIA                 9                 29
  STAGE IIB                 1                  1
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                3                  6
  STAGE IIIB                4                 19
  STAGE IIIC                3                 11
  STAGE IV                  1                 17
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10P LOSS MUTATED    1  7 20  4
  10P LOSS WILD-TYPE  8 22 89 10
D58V4, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  T1                1                  8
  T2                7                 22
  T3               20                 89
  T4                4                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10P LOSS MUTATED   16 10  6
  10P LOSS WILD-TYPE 67 35 26
D58V5, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  N0               16                 67
  N1               10                 35
  N2                6                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  10P LOSS MUTATED   27  2   1  2
  10P LOSS WILD-TYPE 96 20   1 11
D58V6, multiclass
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  M0                27                 96
  M1                 2                 20
  M1A                1                  1
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                    cls
clus                  0  1
  10P LOSS MUTATED   13 19
  10P LOSS WILD-TYPE 61 69
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     13   19
  10P LOSS WILD-TYPE   61   69
        clus
vv       10P LOSS MUTATED 10P LOSS WILD-TYPE
  FEMALE               13                 61
  MALE                 19                 69
[1] 2 2
[1] FALSE
D58V8, binary
                    cls
clus                   0   1
  10P LOSS MUTATED    25   6
  10P LOSS WILD-TYPE 118   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED     25    6
  10P LOSS WILD-TYPE  118    7
                                clus
vv                               10P LOSS MUTATED 10P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        25                118
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
D58V9, binary
                    cls
clus                   0   1
  10P LOSS MUTATED     3  29
  10P LOSS WILD-TYPE   3 127
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10P LOSS MUTATED      3   29
  10P LOSS WILD-TYPE    3  127
     clus
vv    10P LOSS MUTATED 10P LOSS WILD-TYPE
  NO                 3                  3
  YES               29                127
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10P LOSS MUTATED   28  0  0  0
  10P LOSS WILD-TYPE 93  2 12  3
D58V10, multiclass
    clus
vv   10P LOSS MUTATED 10P LOSS WILD-TYPE
  R0               28                 93
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10P LOSS MUTATED       0                         1    20
  10P LOSS WILD-TYPE     1                         2    61
D58V12, multiclass
                           clus
vv                          10P LOSS MUTATED 10P LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   20                 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(59) Variable = 10Q LOSS MUTATION ANALYSIS
D59V1, survival
                    sevent
clus2                 0  1
  10Q LOSS MUTATED   33  3
  10Q LOSS WILD-TYPE 95 19
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                36                114 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
                 3                 19 
$`10Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 
       24.13        13.55        12.72        10.39        32.02        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 
       34.03         6.05        29.98        36.95         1.02        19.99 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A02X 
       13.94        25.97        37.02        12.00        10.98        41.00 
TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
        4.73        13.97        36.00        13.05        10.06       129.27 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       24.13         0.49        17.00        16.34        16.31        16.41 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       11.97        14.86         0.66         0.46        47.08        26.43 

$`10Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        15.39        20.02        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02        17.03         0.99        20.98         6.02        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        15.02         7.10        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       17.69         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        37.51        31.30         0.39         1.02 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 

  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
              0.46               0.39 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            129.27             126.44 
  10Q LOSS MUTATED 10Q LOSS WILD-TYPE 
            16.325             13.990 
[1] "0.5 - 129.3 (16.3)" "0.4 - 126.4 (14.0)"
[1] "hr=" "2"  
D59V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  10Q LOSS MUTATED         6        0        12         1         0         1
  10Q LOSS WILD-TYPE      24        8        26         1         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  10Q LOSS MUTATED            3          5          5        2         1
  10Q LOSS WILD-TYPE          6         18          9       16         8
D59V3, multiclass
            clus
vv           10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  0                  8
  STAGE IIA                12                 26
  STAGE IIB                 1                  1
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                3                  6
  STAGE IIIB                5                 18
  STAGE IIIC                5                  9
  STAGE IV                  2                 16
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  10Q LOSS MUTATED    1  7 26  2
  10Q LOSS WILD-TYPE  8 22 83 12
D59V4, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  T1                1                  8
  T2                7                 22
  T3               26                 83
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  10Q LOSS MUTATED   19 10  7
  10Q LOSS WILD-TYPE 64 35 25
D59V5, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  N0               19                 64
  N1               10                 35
  N2                7                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  10Q LOSS MUTATED   32  2   0  2
  10Q LOSS WILD-TYPE 91 20   2 11
D59V6, multiclass
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  M0                32                 91
  M1                 2                 20
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                    cls
clus                  0  1
  10Q LOSS MUTATED   14 23
  10Q LOSS WILD-TYPE 60 65
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     14   23
  10Q LOSS WILD-TYPE   60   65
        clus
vv       10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  FEMALE               14                 60
  MALE                 23                 65
[1] 2 2
[1] FALSE
D59V8, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED    30   6
  10Q LOSS WILD-TYPE 113   7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED     30    6
  10Q LOSS WILD-TYPE  113    7
                                clus
vv                               10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        30                113
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
D59V9, binary
                    cls
clus                   0   1
  10Q LOSS MUTATED     3  34
  10Q LOSS WILD-TYPE   3 122
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  10Q LOSS MUTATED      3   34
  10Q LOSS WILD-TYPE    3  122
     clus
vv    10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  NO                 3                  3
  YES               34                122
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  10Q LOSS MUTATED   32  0  0  0
  10Q LOSS WILD-TYPE 89  2 12  3
D59V10, multiclass
    clus
vv   10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  R0               32                 89
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  10Q LOSS MUTATED       0                         1    21
  10Q LOSS WILD-TYPE     1                         2    60
D59V12, multiclass
                           clus
vv                          10Q LOSS MUTATED 10Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   21                 60
[1] 3 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 = 11P LOSS MUTATION ANALYSIS
D60V1, survival
                    sevent
clus2                  0   1
  11P LOSS MUTATED    21   1
  11P LOSS WILD-TYPE 107  21
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                22                128 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
                 1                 21 
$`11P LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 
       43.04        14.50        15.39        10.39        32.02         7.07 
TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 
        6.05        32.98         1.02        13.94        12.00        10.98 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-DC-6155 TCGA-DC-6156 TCGA-DT-5265 
       41.00         0.49         0.69        13.97        15.02         5.29 
TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6881 TCGA-F5-6813 
       24.13        17.00        16.41         0.69 

$`11P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       37.74        10.39         8.45        20.02        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       20.98         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        31.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        0.49         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  11P LOSS MUTATED 11P LOSS WILD-TYPE 
              0.49               0.39 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
             43.04             129.27 
  11P LOSS MUTATED 11P LOSS WILD-TYPE 
            13.955             14.940 
[1] "0.5 - 43.0 (14.0)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "2.2"
D60V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11P LOSS MUTATED         6        1         2         0         0         1
  11P LOSS WILD-TYPE      24        7        36         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11P LOSS MUTATED            2          3          5        1         2
  11P LOSS WILD-TYPE          7         20          9       17         7
D60V3, multiclass
            clus
vv           11P LOSS MUTATED 11P LOSS WILD-TYPE
  STAGE I                   6                 24
  STAGE II                  1                  7
  STAGE IIA                 2                 36
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                2                  7
  STAGE IIIB                3                 20
  STAGE IIIC                5                  9
  STAGE IV                  1                 17
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11P LOSS MUTATED    1  6 13  4
  11P LOSS WILD-TYPE  8 23 96 10
D60V4, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  T1                1                  8
  T2                6                 23
  T3               13                 96
  T4                4                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11P LOSS MUTATED    9  7  8
  11P LOSS WILD-TYPE 74 38 24
D60V5, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  N0                9                 74
  N1                7                 38
  N2                8                 24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  11P LOSS MUTATED    19   1   1   3
  11P LOSS WILD-TYPE 104  21   1  10
D60V6, multiclass
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  M0                19                104
  M1                 1                 21
  M1A                1                  1
  MX                 3                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                    cls
clus                  0  1
  11P LOSS MUTATED   11 13
  11P LOSS WILD-TYPE 63 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     11   13
  11P LOSS WILD-TYPE   63   75
        clus
vv       11P LOSS MUTATED 11P LOSS WILD-TYPE
  FEMALE               11                 63
  MALE                 13                 75
[1] 2 2
[1] FALSE
D60V8, binary
                    cls
clus                   0   1
  11P LOSS MUTATED    18   4
  11P LOSS WILD-TYPE 125   9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED     18    4
  11P LOSS WILD-TYPE  125    9
                                clus
vv                               11P LOSS MUTATED 11P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        18                125
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
D60V9, binary
                    cls
clus                   0   1
  11P LOSS MUTATED     2  22
  11P LOSS WILD-TYPE   4 134
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11P LOSS MUTATED      2   22
  11P LOSS WILD-TYPE    4  134
     clus
vv    11P LOSS MUTATED 11P LOSS WILD-TYPE
  NO                 2                  4
  YES               22                134
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  11P LOSS MUTATED    18   0   0   1
  11P LOSS WILD-TYPE 103   2  12   2
D60V10, multiclass
    clus
vv   11P LOSS MUTATED 11P LOSS WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                0                 12
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11P LOSS MUTATED       1                         0    12
  11P LOSS WILD-TYPE     0                         3    69
D60V12, multiclass
                           clus
vv                          11P LOSS MUTATED 11P LOSS WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   12                 69
[1] 3 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 = 11Q LOSS MUTATION ANALYSIS
D61V1, survival
                    sevent
clus2                  0   1
  11Q LOSS MUTATED    23   3
  11Q LOSS WILD-TYPE 105  19
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                26                124 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
                 3                 19 
$`11Q LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       43.04        13.55        19.10        14.50        15.39        10.39 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3896 
       32.02         7.07         2.01         6.05        32.98         1.02 
TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A020 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       13.94        12.00        10.98         0.49         0.69        10.19 
TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF 
       13.97        13.97         7.10        30.05         5.29        24.13 
TCGA-EI-6509 TCGA-EI-6881 
       17.00        16.41 

$`11Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 
        8.45        20.02        36.03        12.00         8.02         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 
        2.01        24.00         1.02        46.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98         1.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03         0.99        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        70.03        64.01        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
       38.96        61.97        41.00        38.04         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.99        12.00        15.02        36.00        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.06       126.44        41.36        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        37.51        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
              0.49               0.39 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
             43.04             129.27 
  11Q LOSS MUTATED 11Q LOSS WILD-TYPE 
            13.745             15.435 
[1] "0.5 - 43.0 (13.7)"  "0.4 - 129.3 (15.4)"
[1] "hr=" "1.4"
D61V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  11Q LOSS MUTATED         8        1         6         0         0         1
  11Q LOSS WILD-TYPE      22        7        32         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  11Q LOSS MUTATED            3          4          4        1         1
  11Q LOSS WILD-TYPE          6         19         10       17         8
D61V3, multiclass
            clus
vv           11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  STAGE I                   8                 22
  STAGE II                  1                  7
  STAGE IIA                 6                 32
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                3                  6
  STAGE IIIB                4                 19
  STAGE IIIC                4                 10
  STAGE IV                  1                 17
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  11Q LOSS MUTATED    1  8 19  2
  11Q LOSS WILD-TYPE  8 21 90 12
D61V4, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  T1                1                  8
  T2                8                 21
  T3               19                 90
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  11Q LOSS MUTATED   15  9  6
  11Q LOSS WILD-TYPE 68 36 26
D61V5, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  N0               15                 68
  N1                9                 36
  N2                6                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  11Q LOSS MUTATED   24  1   0  4
  11Q LOSS WILD-TYPE 99 21   2  9
D61V6, multiclass
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  M0                24                 99
  M1                 1                 21
  M1A                0                  2
  MX                 4                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V7, binary
                    cls
clus                  0  1
  11Q LOSS MUTATED   14 16
  11Q LOSS WILD-TYPE 60 72
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     14   16
  11Q LOSS WILD-TYPE   60   72
        clus
vv       11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  FEMALE               14                 60
  MALE                 16                 72
[1] 2 2
[1] FALSE
D61V8, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED    21   5
  11Q LOSS WILD-TYPE 122   8
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED     21    5
  11Q LOSS WILD-TYPE  122    8
                                clus
vv                               11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        21                122
  RECTAL MUCINOUS ADENOCARCINOMA                5                  8
[1] 2 2
[1] FALSE
D61V9, binary
                    cls
clus                   0   1
  11Q LOSS MUTATED     3  27
  11Q LOSS WILD-TYPE   3 129
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  11Q LOSS MUTATED      3   27
  11Q LOSS WILD-TYPE    3  129
     clus
vv    11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  NO                 3                  3
  YES               27                129
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  11Q LOSS MUTATED   22  0  0  1
  11Q LOSS WILD-TYPE 99  2 12  2
D61V10, multiclass
    clus
vv   11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  R0               22                 99
  R1                0                  2
  R2                0                 12
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D61V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  11Q LOSS MUTATED       1                         0    15
  11Q LOSS WILD-TYPE     0                         3    66
D61V12, multiclass
                           clus
vv                          11Q LOSS MUTATED 11Q LOSS WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   15                 66
[1] 3 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 = 12P LOSS MUTATION ANALYSIS
D62V1, survival
                    sevent
clus2                  0   1
  12P LOSS MUTATED    13   5
  12P LOSS WILD-TYPE 115  17
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                18                132 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
                 5                 17 
$`12P LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3593 TCGA-AG-3728 
       43.04        10.39        14.50        15.39        34.03        29.98 
TCGA-AG-3898 TCGA-AG-A01W TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG 
       48.03        70.03        13.97         7.10        24.13        51.48 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       20.91        17.00        16.31        16.41        14.86         0.66 

$`12P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       37.74         8.45        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        15.02        36.00        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       32.61         0.49         2.40        20.55        19.96        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.39         1.02         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  12P LOSS MUTATED 12P LOSS WILD-TYPE 
              0.66               0.39 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
             70.03             129.27 
  12P LOSS MUTATED 12P LOSS WILD-TYPE 
            16.705             13.595 
[1] "0.7 - 70.0 (16.7)"  "0.4 - 129.3 (13.6)"
[1] "hr=" "1.6"
D62V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12P LOSS MUTATED         2        1         6         0         0         0
  12P LOSS WILD-TYPE      28        7        32         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12P LOSS MUTATED            2          3          3        2         3
  12P LOSS WILD-TYPE          7         20         11       16         6
D62V3, multiclass
            clus
vv           12P LOSS MUTATED 12P LOSS WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  1                  7
  STAGE IIA                 6                 32
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                2                  7
  STAGE IIIB                3                 20
  STAGE IIIC                3                 11
  STAGE IV                  2                 16
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12P LOSS MUTATED    1  2 18  1
  12P LOSS WILD-TYPE  8 27 91 13
D62V4, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  T1                1                  8
  T2                2                 27
  T3               18                 91
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12P LOSS MUTATED    9  8  5
  12P LOSS WILD-TYPE 74 37 27
D62V5, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  N0                9                 74
  N1                8                 37
  N2                5                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12P LOSS MUTATED    16   4   0   2
  12P LOSS WILD-TYPE 107  18   2  11
D62V6, multiclass
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  M0                16                107
  M1                 4                 18
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V7, binary
                    cls
clus                  0  1
  12P LOSS MUTATED   12 10
  12P LOSS WILD-TYPE 62 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     12   10
  12P LOSS WILD-TYPE   62   78
        clus
vv       12P LOSS MUTATED 12P LOSS WILD-TYPE
  FEMALE               12                 62
  MALE                 10                 78
[1] 2 2
[1] FALSE
D62V8, binary
                    cls
clus                   0   1
  12P LOSS MUTATED    21   0
  12P LOSS WILD-TYPE 122  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED     21    0
  12P LOSS WILD-TYPE  122   13
                                clus
vv                               12P LOSS MUTATED 12P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        21                122
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D62V9, binary
                    cls
clus                   0   1
  12P LOSS MUTATED     1  21
  12P LOSS WILD-TYPE   5 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12P LOSS MUTATED      1   21
  12P LOSS WILD-TYPE    5  135
     clus
vv    12P LOSS MUTATED 12P LOSS WILD-TYPE
  NO                 1                  5
  YES               21                135
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12P LOSS MUTATED    18   0   1   0
  12P LOSS WILD-TYPE 103   2  11   3
D62V10, multiclass
    clus
vv   12P LOSS MUTATED 12P LOSS WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D62V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12P LOSS MUTATED       0                         1    13
  12P LOSS WILD-TYPE     1                         2    68
D62V12, multiclass
                           clus
vv                          12P LOSS MUTATED 12P LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   13                 68
[1] 3 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 = 12Q LOSS MUTATION ANALYSIS
D63V1, survival
                    sevent
clus2                  0   1
  12Q LOSS MUTATED    14   4
  12Q LOSS WILD-TYPE 114  18
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                18                132 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
                 4                 18 
$`12Q LOSS MUTATED`
TCGA-AF-2691 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 
       43.04        14.50        15.39        34.03        29.98        48.03 
TCGA-AG-4001 TCGA-AG-A014 TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF 
       36.03        15.95         0.49        13.97         7.10        24.13 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       51.48        17.00        16.31        16.41        14.86         0.66 

$`12Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       37.74        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
        1.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         0.99        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        36.00        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24       129.27        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        0.49         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       31.30         0.39         1.02         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
              0.49               0.39 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
             51.48             129.27 
  12Q LOSS MUTATED 12Q LOSS WILD-TYPE 
            16.360             13.595 
[1] "0.5 - 51.5 (16.4)"  "0.4 - 129.3 (13.6)"
[1] "hr=" "1.5"
D63V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  12Q LOSS MUTATED         3        0         6         0         0         0
  12Q LOSS WILD-TYPE      27        8        32         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  12Q LOSS MUTATED            2          2          2        1         3
  12Q LOSS WILD-TYPE          7         21         12       17         6
D63V3, multiclass
            clus
vv           12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  0                  8
  STAGE IIA                 6                 32
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                2                  7
  STAGE IIIB                2                 21
  STAGE IIIC                2                 12
  STAGE IV                  1                 17
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  12Q LOSS MUTATED    1  3 15  1
  12Q LOSS WILD-TYPE  8 26 94 13
D63V4, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  T1                1                  8
  T2                3                 26
  T3               15                 94
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  12Q LOSS MUTATED    9  7  4
  12Q LOSS WILD-TYPE 74 38 28
D63V5, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  N0                9                 74
  N1                7                 38
  N2                4                 28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  12Q LOSS MUTATED    14   4   0   2
  12Q LOSS WILD-TYPE 109  18   2  11
D63V6, multiclass
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  M0                14                109
  M1                 4                 18
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V7, binary
                    cls
clus                  0  1
  12Q LOSS MUTATED    9 11
  12Q LOSS WILD-TYPE 65 77
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      9   11
  12Q LOSS WILD-TYPE   65   77
        clus
vv       12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  FEMALE                9                 65
  MALE                 11                 77
[1] 2 2
[1] FALSE
D63V8, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED    19   0
  12Q LOSS WILD-TYPE 124  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED     19    0
  12Q LOSS WILD-TYPE  124   13
                                clus
vv                               12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        19                124
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D63V9, binary
                    cls
clus                   0   1
  12Q LOSS MUTATED     1  19
  12Q LOSS WILD-TYPE   5 137
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  12Q LOSS MUTATED      1   19
  12Q LOSS WILD-TYPE    5  137
     clus
vv    12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  NO                 1                  5
  YES               19                137
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  12Q LOSS MUTATED    15   0   1   0
  12Q LOSS WILD-TYPE 106   2  11   3
D63V10, multiclass
    clus
vv   12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  R0               15                106
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D63V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  12Q LOSS MUTATED       0                         0    13
  12Q LOSS WILD-TYPE     1                         3    68
D63V12, multiclass
                           clus
vv                          12Q LOSS MUTATED 12Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   13                 68
[1] 3 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 = 13Q LOSS MUTATION ANALYSIS
D64V1, survival
                    sevent
clus2                  0   1
  13Q LOSS MUTATED     5   1
  13Q LOSS WILD-TYPE 123  21
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 6                144 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 1                 21 
$`13Q LOSS MUTATED`
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-A00Y TCGA-AG-A020 TCGA-DC-6156 TCGA-DY-A0XA 
        2.01         6.05        23.01        10.98        15.02       126.44 

$`13Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
        0.99        20.98        13.94         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
              2.01               0.39 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
            126.44             129.27 
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
             13.00              14.27 
[1] "2.0 - 126.4 (13.0)" "0.4 - 129.3 (14.3)"
[1] "hr=" "1.1"
D64V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  13Q LOSS MUTATED         0        0         4         0         0         1
  13Q LOSS WILD-TYPE      30        8        34         2         2         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  13Q LOSS MUTATED            0          0          1        1         1
  13Q LOSS WILD-TYPE          9         23         13       17         8
D64V3, multiclass
            clus
vv           13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  0                  8
  STAGE IIA                 4                 34
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 1                  4
  STAGE IIIA                0                  9
  STAGE IIIB                0                 23
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 1                  8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  13Q LOSS MUTATED     0   0   7   1
  13Q LOSS WILD-TYPE   9  29 102  13
D64V4, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  T1                0                  9
  T2                0                 29
  T3                7                102
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  13Q LOSS MUTATED    4  1  3
  13Q LOSS WILD-TYPE 79 44 29
D64V5, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  N0                4                 79
  N1                1                 44
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  13Q LOSS MUTATED     6   1   1   0
  13Q LOSS WILD-TYPE 117  21   1  13
D64V6, multiclass
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  M0                 6                117
  M1                 1                 21
  M1A                1                  1
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V7, binary
                    cls
clus                  0  1
  13Q LOSS MUTATED    4  4
  13Q LOSS WILD-TYPE 70 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      4    4
  13Q LOSS WILD-TYPE   70   84
        clus
vv       13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  FEMALE                4                 70
  MALE                  4                 84
[1] 2 2
[1] FALSE
D64V8, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     6   2
  13Q LOSS WILD-TYPE 137  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      6    2
  13Q LOSS WILD-TYPE  137   11
                                clus
vv                               13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         6                137
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
D64V9, binary
                    cls
clus                   0   1
  13Q LOSS MUTATED     0   8
  13Q LOSS WILD-TYPE   6 148
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  13Q LOSS MUTATED      0    8
  13Q LOSS WILD-TYPE    6  148
     clus
vv    13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  NO                 0                  6
  YES                8                148
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  13Q LOSS MUTATED     6   0   1   0
  13Q LOSS WILD-TYPE 115   2  11   3
D64V10, multiclass
    clus
vv   13Q LOSS MUTATED 13Q LOSS WILD-TYPE
  R0                6                115
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D64V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  13Q LOSS MUTATED       0                         0     2
  13Q LOSS WILD-TYPE     1                         3    79
D64V12, multiclass
[1] "Remove cluster labels:" "13Q LOSS MUTATED"      
clus
  13Q LOSS MUTATED 13Q LOSS WILD-TYPE 
                 2                 83 
        TCGA-AF-2687         TCGA-AF-2689         TCGA-AF-2690 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-2691         TCGA-AF-2692         TCGA-AF-2693 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-3400         TCGA-AF-3911         TCGA-AF-3913 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-4110         TCGA-AF-5654         TCGA-AF-6136 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AF-6655         TCGA-AF-6672         TCGA-AH-6544 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6547         TCGA-AH-6643         TCGA-AH-6644 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-AH-6897         TCGA-AH-6903         TCGA-BM-6198 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6619         TCGA-CI-6620         TCGA-CI-6621 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CI-6622         TCGA-CI-6623         TCGA-CI-6624 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-CL-5917         TCGA-CL-5918         TCGA-DC-4745 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-4749         TCGA-DC-5337         TCGA-DC-5869 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6154         TCGA-DC-6155         TCGA-DC-6157 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6158         TCGA-DC-6160         TCGA-DC-6681 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DC-6682         TCGA-DC-6683         TCGA-DT-5265 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DC         TCGA-DY-A1DD         TCGA-DY-A1DE 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-DY-A1DF         TCGA-DY-A1DG         TCGA-DY-A1H8 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EF-5830         TCGA-EF-5831         TCGA-EI-6506 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6507         TCGA-EI-6508         TCGA-EI-6509 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6510         TCGA-EI-6511         TCGA-EI-6512 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6513         TCGA-EI-6514         TCGA-EI-6881 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6882         TCGA-EI-6883         TCGA-EI-6884 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-6885         TCGA-EI-6917         TCGA-EI-7002 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-EI-7004         TCGA-F5-6464         TCGA-F5-6465 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6571         TCGA-F5-6702         TCGA-F5-6810 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6811         TCGA-F5-6812         TCGA-F5-6813 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6814         TCGA-F5-6861         TCGA-F5-6863 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-F5-6864         TCGA-G5-6233         TCGA-G5-6235 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 
        TCGA-G5-6572         TCGA-G5-6641 
"13Q LOSS WILD-TYPE" "13Q LOSS WILD-TYPE" 

Clustering(65) Variable = 14Q LOSS MUTATION ANALYSIS
D65V1, survival
                    sevent
clus2                 0  1
  14Q LOSS MUTATED   50  8
  14Q LOSS WILD-TYPE 78 14
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                58                 92 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
                 8                 14 
$`14Q LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-6672 TCGA-AG-3582 
       17.95        17.23        13.55        37.74        10.39         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 
       46.03        34.03        50.04         6.05         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-4001 
        1.02        17.03        35.01         1.02        48.03        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A026 
       14.04        17.03         6.02        25.97        23.01         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       38.96        38.04         0.49        10.19         6.05         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 
        9.37         4.73        13.97         7.99        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        36.00         7.10        13.05        10.06       129.27 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       51.48        20.55        17.00        16.34        16.31        16.41 
TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       10.78        11.97        31.30         0.39         1.02         0.66 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
        0.76        18.28        55.76        26.43 

$`14Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       24.13        43.04        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
        8.45        15.39        20.02        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
        8.02         7.07         2.01        24.00         1.02         2.01 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       29.98         1.02        32.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 
       13.02        14.01        32.02        19.99        28.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98        13.94        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       10.98        51.98        49.97        61.97        41.00         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 
        0.69         0.72         4.60         1.81         6.97        60.03 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 
       10.98        15.02        12.00        15.02        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       17.69         8.61        11.51        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        9.96        37.51        14.86         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6572 
        0.46        47.08 

  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
              0.39               0.46 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
            129.27             126.44 
  14Q LOSS MUTATED 14Q LOSS WILD-TYPE 
             13.97              14.94 
[1] "0.4 - 129.3 (14.0)" "0.5 - 126.4 (14.9)"
[1] "hr=" "1.1"
D65V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  14Q LOSS MUTATED        10        1        21         0         1         1
  14Q LOSS WILD-TYPE      20        7        17         2         1         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  14Q LOSS MUTATED            5         11          5        7         2
  14Q LOSS WILD-TYPE          4         12          9       11         7
D65V3, multiclass
            clus
vv           14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  STAGE I                  10                 20
  STAGE II                  1                  7
  STAGE IIA                21                 17
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 1                  4
  STAGE IIIA                5                  4
  STAGE IIIB               11                 12
  STAGE IIIC                5                  9
  STAGE IV                  7                 11
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  14Q LOSS MUTATED    3 10 48  4
  14Q LOSS WILD-TYPE  6 19 61 10
D65V4, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  T1                3                  6
  T2               10                 19
  T3               48                 61
  T4                4                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  14Q LOSS MUTATED   32 23 10
  14Q LOSS WILD-TYPE 51 22 22
D65V5, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  N0               32                 51
  N1               23                 22
  N2               10                 22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  14Q LOSS MUTATED   50  9   0  5
  14Q LOSS WILD-TYPE 73 13   2  8
D65V6, multiclass
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  M0                50                 73
  M1                 9                 13
  M1A                0                  2
  MX                 5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V7, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   26 39
  14Q LOSS WILD-TYPE 48 49
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     26   39
  14Q LOSS WILD-TYPE   48   49
        clus
vv       14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  FEMALE               26                 48
  MALE                 39                 49
[1] 2 2
[1] FALSE
D65V8, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED   62  1
  14Q LOSS WILD-TYPE 81 12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED     62    1
  14Q LOSS WILD-TYPE   81   12
                                clus
vv                               14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        62                 81
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D65V9, binary
                    cls
clus                  0  1
  14Q LOSS MUTATED    3 62
  14Q LOSS WILD-TYPE  3 94
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  14Q LOSS MUTATED      3   62
  14Q LOSS WILD-TYPE    3   94
     clus
vv    14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  NO                 3                  3
  YES               62                 94
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  14Q LOSS MUTATED   47  2  3  1
  14Q LOSS WILD-TYPE 74  0  9  2
D65V10, multiclass
    clus
vv   14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  R0               47                 74
  R1                2                  0
  R2                3                  9
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D65V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  14Q LOSS MUTATED       0                         2    34
  14Q LOSS WILD-TYPE     1                         1    47
D65V12, multiclass
                           clus
vv                          14Q LOSS MUTATED 14Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                2                  1
  WHITE                                   34                 47
[1] 3 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 = 15Q LOSS MUTATION ANALYSIS
D66V1, survival
                    sevent
clus2                 0  1
  15Q LOSS MUTATED   55 10
  15Q LOSS WILD-TYPE 73 12
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                65                 85 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
                10                 12 
$`15Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        43.04        13.55        12.72        37.74        14.50 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       10.39        32.02         1.02         2.01        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
       34.03         6.05        19.99        29.98         0.99        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        35.01         1.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03        13.94        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       12.00         1.94        38.96        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
        0.69        10.19         6.05         9.37         7.99        10.98 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD 
       12.99        13.97        36.00        13.05        41.36        57.24 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 
       24.13         0.49         2.40        15.85        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
       11.51        10.78        13.64        11.97        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        1.02         0.66         0.69        18.28        26.43 

$`15Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.95        17.23        19.10        10.39         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 
       20.02        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99         1.02        32.98         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 
       36.95        13.02        14.01        48.03        32.02        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 
        1.02         0.99        20.98         6.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       49.97        61.97         1.45         0.72         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 
        6.05         6.97         4.73        13.97        60.03        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        12.00        15.02         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
       10.06         5.29       126.44       129.27        51.48        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       16.34         8.61        17.46         8.45         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.39         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 
       47.08 

  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
              0.49               0.39 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             57.24             129.27 
  15Q LOSS MUTATED 15Q LOSS WILD-TYPE 
             14.50              14.01 
[1] "0.5 - 57.2 (14.5)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.5"
D66V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  15Q LOSS MUTATED        10        1        21         1         2         2
  15Q LOSS WILD-TYPE      20        7        17         1         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  15Q LOSS MUTATED            4         12          7        9         2
  15Q LOSS WILD-TYPE          5         11          7        9         7
D66V3, multiclass
            clus
vv           15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  STAGE I                  10                 20
  STAGE II                  1                  7
  STAGE IIA                21                 17
  STAGE IIB                 1                  1
  STAGE IIC                 2                  0
  STAGE III                 2                  3
  STAGE IIIA                4                  5
  STAGE IIIB               12                 11
  STAGE IIIC                7                  7
  STAGE IV                  9                  9
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  15Q LOSS MUTATED    4  9 54  5
  15Q LOSS WILD-TYPE  5 20 55  9
D66V4, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  T1                4                  5
  T2                9                 20
  T3               54                 55
  T4                5                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  15Q LOSS MUTATED   34 23 15
  15Q LOSS WILD-TYPE 49 22 17
D66V5, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  N0               34                 49
  N1               23                 22
  N2               15                 17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  15Q LOSS MUTATED   55 10   0  6
  15Q LOSS WILD-TYPE 68 12   2  7
D66V6, multiclass
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  M0                55                 68
  M1                10                 12
  M1A                0                  2
  MX                 6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V7, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   28 44
  15Q LOSS WILD-TYPE 46 44
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     28   44
  15Q LOSS WILD-TYPE   46   44
        clus
vv       15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  FEMALE               28                 46
  MALE                 44                 44
[1] 2 2
[1] FALSE
D66V8, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED   63  6
  15Q LOSS WILD-TYPE 80  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED     63    6
  15Q LOSS WILD-TYPE   80    7
                                clus
vv                               15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        63                 80
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
D66V9, binary
                    cls
clus                  0  1
  15Q LOSS MUTATED    5 67
  15Q LOSS WILD-TYPE  1 89
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  15Q LOSS MUTATED      5   67
  15Q LOSS WILD-TYPE    1   89
     clus
vv    15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  NO                 5                  1
  YES               67                 89
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  15Q LOSS MUTATED   55  1  4  1
  15Q LOSS WILD-TYPE 66  1  8  2
D66V10, multiclass
    clus
vv   15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  R0               55                 66
  R1                1                  1
  R2                4                  8
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D66V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  15Q LOSS MUTATED       0                         2    36
  15Q LOSS WILD-TYPE     1                         1    45
D66V12, multiclass
                           clus
vv                          15Q LOSS MUTATED 15Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                2                  1
  WHITE                                   36                 45
[1] 3 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 = 16P LOSS MUTATION ANALYSIS
D67V1, survival
                    sevent
clus2                  0   1
  16P LOSS MUTATED     6   1
  16P LOSS WILD-TYPE 122  21
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 7                143 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
                 1                 21 
$`16P LOSS MUTATED`
TCGA-AG-3578 TCGA-AG-3609 TCGA-AG-4005 TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 
       32.02        19.99        14.04        13.05         1.02         0.53 
TCGA-G5-6233 
       18.28 

$`16P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        36.03         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       31.30        14.86         0.39         0.66         0.69         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  16P LOSS MUTATED 16P LOSS WILD-TYPE 
              0.53               0.39 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             32.02             129.27 
  16P LOSS MUTATED 16P LOSS WILD-TYPE 
             14.04              14.50 
[1] "0.5 - 32.0 (14.0)"  "0.4 - 129.3 (14.5)"
[1] "hr=" "1.7"
D67V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16P LOSS MUTATED         0        0         6         0         1         0
  16P LOSS WILD-TYPE      30        8        32         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16P LOSS MUTATED            0          0          1        1         0
  16P LOSS WILD-TYPE          9         23         13       17         9
D67V3, multiclass
            clus
vv           16P LOSS MUTATED 16P LOSS WILD-TYPE
  STAGE I                   0                 30
  STAGE II                  0                  8
  STAGE IIA                 6                 32
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                0                 23
  STAGE IIIC                1                 13
  STAGE IV                  1                 17
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16P LOSS MUTATED     0   1   8   0
  16P LOSS WILD-TYPE   9  28 101  14
D67V4, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  T1                0                  9
  T2                1                 28
  T3                8                101
  T4                0                 14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16P LOSS MUTATED    6  0  3
  16P LOSS WILD-TYPE 77 45 29
D67V5, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  N0                6                 77
  N1                0                 45
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  16P LOSS MUTATED     8   1   0   0
  16P LOSS WILD-TYPE 115  21   2  13
D67V6, multiclass
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  M0                 8                115
  M1                 1                 21
  M1A                0                  2
  MX                 0                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V7, binary
                    cls
clus                  0  1
  16P LOSS MUTATED    5  4
  16P LOSS WILD-TYPE 69 84
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      5    4
  16P LOSS WILD-TYPE   69   84
        clus
vv       16P LOSS MUTATED 16P LOSS WILD-TYPE
  FEMALE                5                 69
  MALE                  4                 84
[1] 2 2
[1] FALSE
D67V8, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     7   1
  16P LOSS WILD-TYPE 136  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      7    1
  16P LOSS WILD-TYPE  136   12
                                clus
vv                               16P LOSS MUTATED 16P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                         7                136
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D67V9, binary
                    cls
clus                   0   1
  16P LOSS MUTATED     0   9
  16P LOSS WILD-TYPE   6 147
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16P LOSS MUTATED      0    9
  16P LOSS WILD-TYPE    6  147
     clus
vv    16P LOSS MUTATED 16P LOSS WILD-TYPE
  NO                 0                  6
  YES                9                147
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16P LOSS MUTATED     7   0   0   0
  16P LOSS WILD-TYPE 114   2  12   3
D67V10, multiclass
    clus
vv   16P LOSS MUTATED 16P LOSS WILD-TYPE
  R0                7                114
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D67V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16P LOSS MUTATED       0                         0     4
  16P LOSS WILD-TYPE     1                         3    77
D67V12, multiclass
                           clus
vv                          16P LOSS MUTATED 16P LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    4                 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(68) Variable = 16Q LOSS MUTATION ANALYSIS
D68V1, survival
                    sevent
clus2                  0   1
  16Q LOSS MUTATED    11   1
  16Q LOSS WILD-TYPE 117  21
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                12                138 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
                 1                 21 
$`16Q LOSS MUTATED`
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3732 
       10.39        32.02         6.05        19.99         7.99        32.98 
TCGA-AG-3883 TCGA-AG-4005 TCGA-DC-6682 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        1.02        14.04        13.05         1.02         0.53        18.28 

$`16Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       20.02        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 
       50.04        12.03         0.99        15.95        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       29.98         1.02         0.99         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        28.04        36.03         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30        14.86         0.39         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76         0.46        55.76        47.08        26.43 

  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
              0.53               0.39 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             32.98             129.27 
  16Q LOSS MUTATED 16Q LOSS WILD-TYPE 
             11.72              14.94 
[1] "0.5 - 33.0 (11.7)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "1"  
D68V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  16Q LOSS MUTATED         3        0         6         0         1         0
  16Q LOSS WILD-TYPE      27        8        32         2         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  16Q LOSS MUTATED            0          0          2        2         0
  16Q LOSS WILD-TYPE          9         23         12       16         9
D68V3, multiclass
            clus
vv           16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  0                  8
  STAGE IIA                 6                 32
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 0                  5
  STAGE IIIA                0                  9
  STAGE IIIB                0                 23
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 0                  9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  T1  T2  T3  T4
  16Q LOSS MUTATED     0   4   9   1
  16Q LOSS WILD-TYPE   9  25 100  13
D68V4, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  T1                0                  9
  T2                4                 25
  T3                9                100
  T4                1                 13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  16Q LOSS MUTATED    9  0  5
  16Q LOSS WILD-TYPE 74 45 27
D68V5, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  N0                9                 74
  N1                0                 45
  N2                5                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  16Q LOSS MUTATED    12   1   0   1
  16Q LOSS WILD-TYPE 111  21   2  12
D68V6, multiclass
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  M0                12                111
  M1                 1                 21
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V7, binary
                    cls
clus                  0  1
  16Q LOSS MUTATED    7  7
  16Q LOSS WILD-TYPE 67 81
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      7    7
  16Q LOSS WILD-TYPE   67   81
        clus
vv       16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  FEMALE                7                 67
  MALE                  7                 81
[1] 2 2
[1] FALSE
D68V8, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED    12   1
  16Q LOSS WILD-TYPE 131  12
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED     12    1
  16Q LOSS WILD-TYPE  131   12
                                clus
vv                               16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        12                131
  RECTAL MUCINOUS ADENOCARCINOMA                1                 12
[1] 2 2
[1] FALSE
D68V9, binary
                    cls
clus                   0   1
  16Q LOSS MUTATED     1  13
  16Q LOSS WILD-TYPE   5 143
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  16Q LOSS MUTATED      1   13
  16Q LOSS WILD-TYPE    5  143
     clus
vv    16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  NO                 1                  5
  YES               13                143
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  16Q LOSS MUTATED    11   0   0   0
  16Q LOSS WILD-TYPE 110   2  12   3
D68V10, multiclass
    clus
vv   16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  R0               11                110
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D68V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  16Q LOSS MUTATED       0                         0     5
  16Q LOSS WILD-TYPE     1                         3    76
D68V12, multiclass
                           clus
vv                          16Q LOSS MUTATED 16Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                    5                 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(69) Variable = 17P LOSS MUTATION ANALYSIS
D69V1, survival
                    sevent
clus2                 0  1
  17P LOSS MUTATED   80 14
  17P LOSS WILD-TYPE 48  8
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                94                 56 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
                14                  8 
$`17P LOSS MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 
       37.74        14.50        15.39        20.02        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        7.07         1.02        24.00        34.03         2.01        50.04 
TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        0.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3883 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
        1.02        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 
       28.04        36.03        14.04         1.02        17.03        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02        15.95         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
       12.00        31.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 
       41.00         0.49         0.69         0.72         4.60        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.05         6.97        13.97         7.99        11.01 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       13.97         7.10        30.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
        2.40        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 
       16.31        16.41        11.51        10.78        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 
        9.96        37.51        31.30        14.86         0.39         0.69 
TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.53         0.76         0.46        55.76 

$`17P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 
       24.13        10.39         8.45        10.39        36.03         8.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
        2.01         1.02        46.03        12.03         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
       19.99        19.99        29.98         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 
       17.03        13.02        14.01         0.99        20.98        36.03 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        9.07        10.98        49.97        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
        1.45         1.81         9.37         4.73        60.03        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       15.02        12.99        12.00        15.02        36.00        12.95 
TCGA-DC-6682 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 
       13.05        32.61        20.55        19.96        15.85         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 
       13.64        17.46         1.02         0.66         1.12        18.28 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  17P LOSS MUTATED 17P LOSS WILD-TYPE 
              0.39               0.66 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            129.27              61.97 
  17P LOSS MUTATED 17P LOSS WILD-TYPE 
            14.270             14.515 
[1] "0.4 - 129.3 (14.3)" "0.7 - 62.0 (14.5)" 
[1] "hr=" "1.1"
D69V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17P LOSS MUTATED        15        5        28         2         1         3
  17P LOSS WILD-TYPE      15        3        10         0         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17P LOSS MUTATED            5         15         10       12         6
  17P LOSS WILD-TYPE          4          8          4        6         3
D69V3, multiclass
            clus
vv           17P LOSS MUTATED 17P LOSS WILD-TYPE
  STAGE I                  15                 15
  STAGE II                  5                  3
  STAGE IIA                28                 10
  STAGE IIB                 2                  0
  STAGE IIC                 1                  1
  STAGE III                 3                  2
  STAGE IIIA                5                  4
  STAGE IIIB               15                  8
  STAGE IIIC               10                  4
  STAGE IV                 12                  6
  STAGE IVA                 6                  3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17P LOSS MUTATED    2 18 73 11
  17P LOSS WILD-TYPE  7 11 36  3
D69V4, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  T1                2                  7
  T2               18                 11
  T3               73                 36
  T4               11                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17P LOSS MUTATED   53 30 20
  17P LOSS WILD-TYPE 30 15 12
D69V5, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  N0               53                 30
  N1               30                 15
  N2               20                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  17P LOSS MUTATED   78 16   0  9
  17P LOSS WILD-TYPE 45  6   2  4
D69V6, multiclass
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  M0                78                 45
  M1                16                  6
  M1A                0                  2
  MX                 9                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V7, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   49 55
  17P LOSS WILD-TYPE 25 33
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     49   55
  17P LOSS WILD-TYPE   25   33
        clus
vv       17P LOSS MUTATED 17P LOSS WILD-TYPE
  FEMALE               49                 25
  MALE                 55                 33
[1] 2 2
[1] FALSE
D69V8, binary
                    cls
clus                  0  1
  17P LOSS MUTATED   94  6
  17P LOSS WILD-TYPE 49  7
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED     94    6
  17P LOSS WILD-TYPE   49    7
                                clus
vv                               17P LOSS MUTATED 17P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        94                 49
  RECTAL MUCINOUS ADENOCARCINOMA                6                  7
[1] 2 2
[1] FALSE
D69V9, binary
                    cls
clus                   0   1
  17P LOSS MUTATED     4 100
  17P LOSS WILD-TYPE   2  56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17P LOSS MUTATED      4  100
  17P LOSS WILD-TYPE    2   56
     clus
vv    17P LOSS MUTATED 17P LOSS WILD-TYPE
  NO                 4                  2
  YES              100                 56
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  17P LOSS MUTATED   74  2  9  2
  17P LOSS WILD-TYPE 47  0  3  1
D69V10, multiclass
    clus
vv   17P LOSS MUTATED 17P LOSS WILD-TYPE
  R0               74                 47
  R1                2                  0
  R2                9                  3
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D69V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17P LOSS MUTATED       1                         0    54
  17P LOSS WILD-TYPE     0                         3    27
D69V12, multiclass
                           clus
vv                          17P LOSS MUTATED 17P LOSS WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   54                 27
[1] 3 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 = 17Q LOSS MUTATION ANALYSIS
D70V1, survival
                    sevent
clus2                  0   1
  17Q LOSS MUTATED    18   5
  17Q LOSS WILD-TYPE 110  17
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                23                127 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
                 5                 17 
$`17Q LOSS MUTATED`
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3999 
       14.50        15.39         1.02         1.02        32.02        28.04 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A02X TCGA-BM-6198 
       13.94        25.97        12.00        51.98        41.00        10.19 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 
       13.97         7.10         5.29        24.13         0.49         2.40 
TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6814 
       17.69        16.41        11.51        14.86         0.53 

$`17Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       12.72        37.74        10.39         8.45        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       35.01        14.01        48.03        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02        17.03         0.99        20.98         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N 
       37.02        15.95        36.03         9.07         1.02        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       15.02        12.99        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.31         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       37.51        31.30         0.39         1.02         0.66         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
              0.49               0.39 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             51.98             129.27 
  17Q LOSS MUTATED 17Q LOSS WILD-TYPE 
             13.97              15.02 
[1] "0.5 - 52.0 (14.0)"  "0.4 - 129.3 (15.0)"
[1] "hr=" "2.3"
D70V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  17Q LOSS MUTATED         4        1         5         1         1         0
  17Q LOSS WILD-TYPE      26        7        33         1         1         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  17Q LOSS MUTATED            2          4          2        3         2
  17Q LOSS WILD-TYPE          7         19         12       15         7
D70V3, multiclass
            clus
vv           17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  STAGE I                   4                 26
  STAGE II                  1                  7
  STAGE IIA                 5                 33
  STAGE IIB                 1                  1
  STAGE IIC                 1                  1
  STAGE III                 0                  5
  STAGE IIIA                2                  7
  STAGE IIIB                4                 19
  STAGE IIIC                2                 12
  STAGE IV                  3                 15
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  17Q LOSS MUTATED    0  6 16  3
  17Q LOSS WILD-TYPE  9 23 93 11
D70V4, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  T1                0                  9
  T2                6                 23
  T3               16                 93
  T4                3                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  17Q LOSS MUTATED   12  8  5
  17Q LOSS WILD-TYPE 71 37 27
D70V5, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  N0               12                 71
  N1                8                 37
  N2                5                 27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  17Q LOSS MUTATED    18   4   0   2
  17Q LOSS WILD-TYPE 105  18   2  11
D70V6, multiclass
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  M0                18                105
  M1                 4                 18
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V7, binary
                    cls
clus                  0  1
  17Q LOSS MUTATED   10 15
  17Q LOSS WILD-TYPE 64 73
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     10   15
  17Q LOSS WILD-TYPE   64   73
        clus
vv       17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  FEMALE               10                 64
  MALE                 15                 73
[1] 2 2
[1] FALSE
D70V8, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED    22   2
  17Q LOSS WILD-TYPE 121  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED     22    2
  17Q LOSS WILD-TYPE  121   11
                                clus
vv                               17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        22                121
  RECTAL MUCINOUS ADENOCARCINOMA                2                 11
[1] 2 2
[1] FALSE
D70V9, binary
                    cls
clus                   0   1
  17Q LOSS MUTATED     2  23
  17Q LOSS WILD-TYPE   4 133
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  17Q LOSS MUTATED      2   23
  17Q LOSS WILD-TYPE    4  133
     clus
vv    17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  NO                 2                  4
  YES               23                133
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  17Q LOSS MUTATED    19   0   3   1
  17Q LOSS WILD-TYPE 102   2   9   2
D70V10, multiclass
    clus
vv   17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  R0               19                102
  R1                0                  2
  R2                3                  9
  RX                1                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D70V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  17Q LOSS MUTATED       1                         0    13
  17Q LOSS WILD-TYPE     0                         3    68
D70V12, multiclass
                           clus
vv                          17Q LOSS MUTATED 17Q LOSS WILD-TYPE
  ASIAN                                    1                  0
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   13                 68
[1] 3 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 = 18P LOSS MUTATION ANALYSIS
D71V1, survival
                    sevent
clus2                  0   1
  18P LOSS MUTATED   100  16
  18P LOSS WILD-TYPE  28   6
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
               116                 34 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
                16                  6 
$`18P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 
       37.74        10.39        14.50        15.39        20.02        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       12.00         7.07         1.02         2.01        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       34.03        50.04         0.99        15.95        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       36.95        17.03        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        36.03         1.02        17.03         0.99 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
        9.07         1.02        12.00        31.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       51.98         1.94        41.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        20.55        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       13.64        11.97        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        1.02         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$`18P LOSS WILD-TYPE`
TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3586 
       19.10         8.45        10.39        32.02         8.02         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 
        2.01        12.03         6.05        19.99         0.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A01Y 
       13.02        14.01        14.04        20.98        36.03        64.01 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 
       49.97        38.96        61.97         1.45         1.81         5.29 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       32.61        19.96        20.91         8.61        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
        9.96         0.53         1.12        47.08 

  18P LOSS MUTATED 18P LOSS WILD-TYPE 
              0.39               0.53 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            129.27              64.01 
  18P LOSS MUTATED 18P LOSS WILD-TYPE 
            15.020             12.525 
[1] "0.4 - 129.3 (15.0)" "0.5 - 64.0 (12.5)" 
[1] "hr=" "1.3"
D71V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18P LOSS MUTATED        21        5        31         2         2         2
  18P LOSS WILD-TYPE       9        3         7         0         0         3
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18P LOSS MUTATED            6         20         11       15         8
  18P LOSS WILD-TYPE          3          3          3        3         1
D71V3, multiclass
            clus
vv           18P LOSS MUTATED 18P LOSS WILD-TYPE
  STAGE I                  21                  9
  STAGE II                  5                  3
  STAGE IIA                31                  7
  STAGE IIB                 2                  0
  STAGE IIC                 2                  0
  STAGE III                 2                  3
  STAGE IIIA                6                  3
  STAGE IIIB               20                  3
  STAGE IIIC               11                  3
  STAGE IV                 15                  3
  STAGE IVA                 8                  1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18P LOSS MUTATED    5 21 88 11
  18P LOSS WILD-TYPE  4  8 21  3
D71V4, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  T1                5                  4
  T2               21                  8
  T3               88                 21
  T4               11                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18P LOSS MUTATED   62 37 25
  18P LOSS WILD-TYPE 21  8  7
D71V5, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  N0               62                 21
  N1               37                  8
  N2               25                  7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  18P LOSS MUTATED   93 20   2  9
  18P LOSS WILD-TYPE 30  2   0  4
D71V6, multiclass
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  M0                93                 30
  M1                20                  2
  M1A                2                  0
  MX                 9                  4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V7, binary
                    cls
clus                  0  1
  18P LOSS MUTATED   57 68
  18P LOSS WILD-TYPE 17 20
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED     57   68
  18P LOSS WILD-TYPE   17   20
        clus
vv       18P LOSS MUTATED 18P LOSS WILD-TYPE
  FEMALE               57                 17
  MALE                 68                 20
[1] 2 2
[1] FALSE
D71V8, binary
                    cls
clus                   0   1
  18P LOSS MUTATED   116   7
  18P LOSS WILD-TYPE  27   6
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED    116    7
  18P LOSS WILD-TYPE   27    6
                                clus
vv                               18P LOSS MUTATED 18P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       116                 27
  RECTAL MUCINOUS ADENOCARCINOMA                7                  6
[1] 2 2
[1] FALSE
D71V9, binary
                    cls
clus                   0   1
  18P LOSS MUTATED     5 120
  18P LOSS WILD-TYPE   1  36
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18P LOSS MUTATED      5  120
  18P LOSS WILD-TYPE    1   36
     clus
vv    18P LOSS MUTATED 18P LOSS WILD-TYPE
  NO                 5                  1
  YES              120                 36
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  18P LOSS MUTATED   93  2 11  2
  18P LOSS WILD-TYPE 28  0  1  1
D71V10, multiclass
    clus
vv   18P LOSS MUTATED 18P LOSS WILD-TYPE
  R0               93                 28
  R1                2                  0
  R2               11                  1
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D71V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18P LOSS MUTATED       0                         3    65
  18P LOSS WILD-TYPE     1                         0    16
D71V12, multiclass
                           clus
vv                          18P LOSS MUTATED 18P LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   65                 16
[1] 3 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 = 18Q LOSS MUTATION ANALYSIS
D72V1, survival
                    sevent
clus2                  0   1
  18Q LOSS MUTATED   107  18
  18Q LOSS WILD-TYPE  21   4
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
               125                 25 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
                18                  4 
$`18Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        15.39        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 
       24.00        46.03        34.03         2.01        50.04         0.99 
TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       32.98         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 
       36.03        14.04         1.02        17.03         0.99        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       51.98         1.94        41.00        38.04         0.49         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.64        11.97         8.45        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       14.86         0.39         1.02         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`18Q LOSS WILD-TYPE`
TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3600 
        8.45        10.39         8.02         1.02        12.03         6.05 
TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 
       19.99         0.99        13.02        14.01        20.98        36.03 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 
       49.97        38.96        61.97         1.45         1.81         5.29 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 
       32.61        19.96         8.61        17.46         9.96         0.53 
TCGA-F5-6861 
        1.12 

  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
              0.39               0.53 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
            129.27              61.97 
  18Q LOSS MUTATED 18Q LOSS WILD-TYPE 
             15.02              10.39 
[1] "0.4 - 129.3 (15.0)" "0.5 - 62.0 (10.4)" 
[1] "hr=" "1.4"
D72V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  18Q LOSS MUTATED        22        6        34         2         2         3
  18Q LOSS WILD-TYPE       8        2         4         0         0         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  18Q LOSS MUTATED            6         21         11       16         9
  18Q LOSS WILD-TYPE          3          2          3        2         0
D72V3, multiclass
            clus
vv           18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  STAGE I                  22                  8
  STAGE II                  6                  2
  STAGE IIA                34                  4
  STAGE IIB                 2                  0
  STAGE IIC                 2                  0
  STAGE III                 3                  2
  STAGE IIIA                6                  3
  STAGE IIIB               21                  2
  STAGE IIIC               11                  3
  STAGE IV                 16                  2
  STAGE IVA                 9                  0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  18Q LOSS MUTATED    5 22 95 12
  18Q LOSS WILD-TYPE  4  7 14  2
D72V4, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  T1                5                  4
  T2               22                  7
  T3               95                 14
  T4               12                  2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  18Q LOSS MUTATED   67 39 27
  18Q LOSS WILD-TYPE 16  6  5
D72V5, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  N0               67                 16
  N1               39                  6
  N2               27                  5
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  18Q LOSS MUTATED   100  21   2  10
  18Q LOSS WILD-TYPE  23   1   0   3
D72V6, multiclass
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  M0               100                 23
  M1                21                  1
  M1A                2                  0
  MX                10                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V7, binary
                    cls
clus                  0  1
  18Q LOSS MUTATED   63 72
  18Q LOSS WILD-TYPE 11 16
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED     63   72
  18Q LOSS WILD-TYPE   11   16
        clus
vv       18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  FEMALE               63                 11
  MALE                 72                 16
[1] 2 2
[1] FALSE
D72V8, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED   121  10
  18Q LOSS WILD-TYPE  22   3
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED    121   10
  18Q LOSS WILD-TYPE   22    3
                                clus
vv                               18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       121                 22
  RECTAL MUCINOUS ADENOCARCINOMA               10                  3
[1] 2 2
[1] FALSE
D72V9, binary
                    cls
clus                   0   1
  18Q LOSS MUTATED     5 130
  18Q LOSS WILD-TYPE   1  26
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  18Q LOSS MUTATED      5  130
  18Q LOSS WILD-TYPE    1   26
     clus
vv    18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  NO                 5                  1
  YES              130                 26
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  18Q LOSS MUTATED   100   2  11   2
  18Q LOSS WILD-TYPE  21   0   1   1
D72V10, multiclass
    clus
vv   18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  R0              100                 21
  R1                2                  0
  R2               11                  1
  RX                2                  1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D72V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  18Q LOSS MUTATED       0                         3    69
  18Q LOSS WILD-TYPE     1                         0    12
D72V12, multiclass
                           clus
vv                          18Q LOSS MUTATED 18Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                3                  0
  WHITE                                   69                 12
[1] 3 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 = 19P LOSS MUTATION ANALYSIS
D73V1, survival
                    sevent
clus2                  0   1
  19P LOSS MUTATED    15   4
  19P LOSS WILD-TYPE 113  18
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                19                131 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
                 4                 18 
$`19P LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3608 TCGA-AG-4008 TCGA-AG-A016 TCGA-AG-A01Y 
       24.13        14.50        15.95        17.03         9.07        64.01 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A1DF TCGA-DY-A1DG 
        4.73        11.01        12.99        13.97        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 
        0.49        16.34        11.51        11.97        31.30        14.86 
TCGA-G5-6233 
       18.28 

$`19P LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
       36.03         1.02        12.00        31.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.03         7.99        10.98        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.31        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  19P LOSS MUTATED 19P LOSS WILD-TYPE 
              0.49               0.39 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             64.01             129.27 
  19P LOSS MUTATED 19P LOSS WILD-TYPE 
             14.86              14.01 
[1] "0.5 - 64.0 (14.9)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.5"
D73V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19P LOSS MUTATED         2        1         5         1         2         1
  19P LOSS WILD-TYPE      28        7        33         1         0         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19P LOSS MUTATED            1          2          2        2         3
  19P LOSS WILD-TYPE          8         21         12       16         6
D73V3, multiclass
            clus
vv           19P LOSS MUTATED 19P LOSS WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  1                  7
  STAGE IIA                 5                 33
  STAGE IIB                 1                  1
  STAGE IIC                 2                  0
  STAGE III                 1                  4
  STAGE IIIA                1                  8
  STAGE IIIB                2                 21
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19P LOSS MUTATED    0  3 17  2
  19P LOSS WILD-TYPE  9 26 92 12
D73V4, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  T1                0                  9
  T2                3                 26
  T3               17                 92
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19P LOSS MUTATED   10  5  7
  19P LOSS WILD-TYPE 73 40 25
D73V5, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  N0               10                 73
  N1                5                 40
  N2                7                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19P LOSS MUTATED    17   4   0   1
  19P LOSS WILD-TYPE 106  18   2  12
D73V6, multiclass
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  M0                17                106
  M1                 4                 18
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V7, binary
                    cls
clus                  0  1
  19P LOSS MUTATED   10 12
  19P LOSS WILD-TYPE 64 76
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     10   12
  19P LOSS WILD-TYPE   64   76
        clus
vv       19P LOSS MUTATED 19P LOSS WILD-TYPE
  FEMALE               10                 64
  MALE                 12                 76
[1] 2 2
[1] FALSE
D73V8, binary
                    cls
clus                   0   1
  19P LOSS MUTATED    20   0
  19P LOSS WILD-TYPE 123  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED     20    0
  19P LOSS WILD-TYPE  123   13
                                clus
vv                               19P LOSS MUTATED 19P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        20                123
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D73V9, binary
                    cls
clus                   0   1
  19P LOSS MUTATED     1  21
  19P LOSS WILD-TYPE   5 135
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19P LOSS MUTATED      1   21
  19P LOSS WILD-TYPE    5  135
     clus
vv    19P LOSS MUTATED 19P LOSS WILD-TYPE
  NO                 1                  5
  YES               21                135
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19P LOSS MUTATED    17   0   1   0
  19P LOSS WILD-TYPE 104   2  11   3
D73V10, multiclass
    clus
vv   19P LOSS MUTATED 19P LOSS WILD-TYPE
  R0               17                104
  R1                0                  2
  R2                1                 11
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D73V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19P LOSS MUTATED       0                         1    14
  19P LOSS WILD-TYPE     1                         2    67
D73V12, multiclass
                           clus
vv                          19P LOSS MUTATED 19P LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   14                 67
[1] 3 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 = 19Q LOSS MUTATION ANALYSIS
D74V1, survival
                    sevent
clus2                  0   1
  19Q LOSS MUTATED    15   3
  19Q LOSS WILD-TYPE 113  19
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                18                132 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
                 3                 19 
$`19Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AG-3608 TCGA-AG-4001 TCGA-AG-A011 TCGA-AG-A01Y 
       24.13        14.50        15.95        36.03        37.02        64.01 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DY-A1DF TCGA-EF-5830 
        4.73        10.98        11.01        12.99        24.13         0.49 
TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6233 
       16.34        11.51        11.97        31.30        14.86        18.28 

$`19Q LOSS WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 
       50.04        12.03         6.05         0.99        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
        9.07         1.02        12.00        31.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
       13.97        60.03         7.99        15.02        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       37.51         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76         0.46        55.76        47.08        26.43 

  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
              0.49               0.39 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
             64.01             129.27 
  19Q LOSS MUTATED 19Q LOSS WILD-TYPE 
            15.405             13.990 
[1] "0.5 - 64.0 (15.4)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.1"
D74V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  19Q LOSS MUTATED         2        1         6         1         2         1
  19Q LOSS WILD-TYPE      28        7        32         1         0         4
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  19Q LOSS MUTATED            0          3          2        1         2
  19Q LOSS WILD-TYPE          9         20         12       17         7
D74V3, multiclass
            clus
vv           19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  STAGE I                   2                 28
  STAGE II                  1                  7
  STAGE IIA                 6                 32
  STAGE IIB                 1                  1
  STAGE IIC                 2                  0
  STAGE III                 1                  4
  STAGE IIIA                0                  9
  STAGE IIIB                3                 20
  STAGE IIIC                2                 12
  STAGE IV                  1                 17
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  19Q LOSS MUTATED    0  2 17  2
  19Q LOSS WILD-TYPE  9 27 92 12
D74V4, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  T1                0                  9
  T2                2                 27
  T3               17                 92
  T4                2                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  19Q LOSS MUTATED   11  4  6
  19Q LOSS WILD-TYPE 72 41 26
D74V5, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  N0               11                 72
  N1                4                 41
  N2                6                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  19Q LOSS MUTATED    18   2   0   1
  19Q LOSS WILD-TYPE 105  20   2  12
D74V6, multiclass
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  M0                18                105
  M1                 2                 20
  M1A                0                  2
  MX                 1                 12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V7, binary
                    cls
clus                  0  1
  19Q LOSS MUTATED   11 10
  19Q LOSS WILD-TYPE 63 78
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     11   10
  19Q LOSS WILD-TYPE   63   78
        clus
vv       19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  FEMALE               11                 63
  MALE                 10                 78
[1] 2 2
[1] FALSE
D74V8, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED    19   0
  19Q LOSS WILD-TYPE 124  13
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED     19    0
  19Q LOSS WILD-TYPE  124   13
                                clus
vv                               19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        19                124
  RECTAL MUCINOUS ADENOCARCINOMA                0                 13
[1] 2 2
[1] FALSE
D74V9, binary
                    cls
clus                   0   1
  19Q LOSS MUTATED     1  20
  19Q LOSS WILD-TYPE   5 136
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  19Q LOSS MUTATED      1   20
  19Q LOSS WILD-TYPE    5  136
     clus
vv    19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  NO                 1                  5
  YES               20                136
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  19Q LOSS MUTATED    18   0   0   0
  19Q LOSS WILD-TYPE 103   2  12   3
D74V10, multiclass
    clus
vv   19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  R0               18                103
  R1                0                  2
  R2                0                 12
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D74V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  19Q LOSS MUTATED       0                         1    13
  19Q LOSS WILD-TYPE     1                         2    68
D74V12, multiclass
                           clus
vv                          19Q LOSS MUTATED 19Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   13                 68
[1] 3 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 = 20P LOSS MUTATION ANALYSIS
D75V1, survival
                    sevent
clus2                  0   1
  20P LOSS MUTATED    18   5
  20P LOSS WILD-TYPE 110  17
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                23                127 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
                 5                 17 
$`20P LOSS MUTATED`
TCGA-AF-4110 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-3902 TCGA-AG-4022 
       14.50        36.03        32.02         6.05        32.02         0.99 
TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       13.94         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6683 TCGA-DY-A1DD 
        1.94        38.96         4.73        11.01        10.06        57.24 
TCGA-EI-6511 TCGA-EI-6881 TCGA-F5-6571 TCGA-F5-6702 TCGA-G5-6641 
       15.85        16.41        31.30        14.86        26.43 

$`20P LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       10.39        12.00         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        48.03        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        20.98         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 
       23.01        37.02        15.95        36.03         9.07        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 
       17.00        18.28        17.69        16.34        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        9.96        37.51         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  20P LOSS MUTATED 20P LOSS WILD-TYPE 
              0.99               0.39 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             70.03             129.27 
  20P LOSS MUTATED 20P LOSS WILD-TYPE 
             15.85              13.97 
[1] "1.0 - 70.0 (15.8)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.2"
D75V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  20P LOSS MUTATED         3        5         4         0         0         0
  20P LOSS WILD-TYPE      27        3        34         2         2         5
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  20P LOSS MUTATED            2          5          2        2         2
  20P LOSS WILD-TYPE          7         18         12       16         7
D75V3, multiclass
            clus
vv           20P LOSS MUTATED 20P LOSS WILD-TYPE
  STAGE I                   3                 27
  STAGE II                  5                  3
  STAGE IIA                 4                 34
  STAGE IIB                 0                  2
  STAGE IIC                 0                  2
  STAGE III                 0                  5
  STAGE IIIA                2                  7
  STAGE IIIB                5                 18
  STAGE IIIC                2                 12
  STAGE IV                  2                 16
  STAGE IVA                 2                  7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  20P LOSS MUTATED    1  5 16  3
  20P LOSS WILD-TYPE  8 24 93 11
D75V4, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  T1                1                  8
  T2                5                 24
  T3               16                 93
  T4                3                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  20P LOSS MUTATED   13  9  3
  20P LOSS WILD-TYPE 70 36 29
D75V5, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  N0               13                 70
  N1                9                 36
  N2                3                 29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                  M0  M1 M1A  MX
  20P LOSS MUTATED    20   3   0   2
  20P LOSS WILD-TYPE 103  19   2  11
D75V6, multiclass
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  M0                20                103
  M1                 3                 19
  M1A                0                  2
  MX                 2                 11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V7, binary
                    cls
clus                  0  1
  20P LOSS MUTATED   12 13
  20P LOSS WILD-TYPE 62 75
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     12   13
  20P LOSS WILD-TYPE   62   75
        clus
vv       20P LOSS MUTATED 20P LOSS WILD-TYPE
  FEMALE               12                 62
  MALE                 13                 75
[1] 2 2
[1] FALSE
D75V8, binary
                    cls
clus                   0   1
  20P LOSS MUTATED    21   3
  20P LOSS WILD-TYPE 122  10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED     21    3
  20P LOSS WILD-TYPE  122   10
                                clus
vv                               20P LOSS MUTATED 20P LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        21                122
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 2 2
[1] FALSE
D75V9, binary
                    cls
clus                   0   1
  20P LOSS MUTATED     0  25
  20P LOSS WILD-TYPE   6 131
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  20P LOSS MUTATED      0   25
  20P LOSS WILD-TYPE    6  131
     clus
vv    20P LOSS MUTATED 20P LOSS WILD-TYPE
  NO                 0                  6
  YES               25                131
[1] 2 2
[1] FALSE
                    vv
clus                  R0  R1  R2  RX
  20P LOSS MUTATED    19   1   3   0
  20P LOSS WILD-TYPE 102   1   9   3
D75V10, multiclass
    clus
vv   20P LOSS MUTATED 20P LOSS WILD-TYPE
  R0               19                102
  R1                1                  1
  R2                3                  9
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D75V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  20P LOSS MUTATED       0                         0    10
  20P LOSS WILD-TYPE     1                         3    71
D75V12, multiclass
                           clus
vv                          20P LOSS MUTATED 20P LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   10                 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(76) Variable = 21Q LOSS MUTATION ANALYSIS
D76V1, survival
                    sevent
clus2                 0  1
  21Q LOSS MUTATED   50 10
  21Q LOSS WILD-TYPE 78 12
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                60                 90 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
                10                 12 
$`21Q LOSS MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       24.13        17.95        17.23        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 
       10.39        12.00         7.07         1.02        24.00        46.03 
TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3728 TCGA-AG-3882 
       34.03        12.03         6.05        19.99        29.98        19.99 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4008 
       17.03         1.02        48.03        19.99        36.03        17.03 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02G 
       12.00        31.00        70.03        64.01        10.98        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
       61.97        41.00         0.69         4.73        13.97        10.98 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD 
       13.97         7.10        13.05        10.06       126.44        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 
      129.27        51.48        32.61        20.55        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       17.69        16.34        16.41        11.97         8.45        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.39         0.66         0.53         0.76        18.28        26.43 

$`21Q LOSS WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       43.04        13.55        19.10        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 
        8.45        36.03        32.02         8.02         2.01         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
        2.01        50.04         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        0.99         1.02        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 
       36.95        13.02        35.01        14.01        32.02        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 
        1.02        51.98        49.97         1.94        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.97         9.37        60.03         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       15.02        12.99        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-EF-5830 TCGA-EF-5831 
       12.95         5.29        41.36        24.13         0.49         2.40 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       19.96        17.00        18.28        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       10.78        13.64        17.46         9.96        37.51        14.86 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.02         0.69         1.12         0.46        55.76        47.08 

  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
              0.39               0.46 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
            129.27              60.03 
  21Q LOSS MUTATED 21Q LOSS WILD-TYPE 
             17.13              12.97 
[1] "0.4 - 129.3 (17.1)" "0.5 - 60.0 (13.0)" 
[1] "hr=" "1.3"
D76V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  21Q LOSS MUTATED         9        4        15         0         1         3
  21Q LOSS WILD-TYPE      21        4        23         2         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  21Q LOSS MUTATED            6         12          6        7         3
  21Q LOSS WILD-TYPE          3         11          8       11         6
D76V3, multiclass
            clus
vv           21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  STAGE I                   9                 21
  STAGE II                  4                  4
  STAGE IIA                15                 23
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 3                  2
  STAGE IIIA                6                  3
  STAGE IIIB               12                 11
  STAGE IIIC                6                  8
  STAGE IV                  7                 11
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  21Q LOSS MUTATED    1 15 46  4
  21Q LOSS WILD-TYPE  8 14 63 10
D76V4, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  T1                1                  8
  T2               15                 14
  T3               46                 63
  T4                4                 10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  21Q LOSS MUTATED   29 23 14
  21Q LOSS WILD-TYPE 54 22 18
D76V5, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  N0               29                 54
  N1               23                 22
  N2               14                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  21Q LOSS MUTATED   54  7   0  5
  21Q LOSS WILD-TYPE 69 15   2  8
D76V6, multiclass
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  M0                54                 69
  M1                 7                 15
  M1A                0                  2
  MX                 5                  8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V7, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   32 34
  21Q LOSS WILD-TYPE 42 54
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     32   34
  21Q LOSS WILD-TYPE   42   54
        clus
vv       21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  FEMALE               32                 42
  MALE                 34                 54
[1] 2 2
[1] FALSE
D76V8, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED   60  3
  21Q LOSS WILD-TYPE 83 10
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED     60    3
  21Q LOSS WILD-TYPE   83   10
                                clus
vv                               21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        60                 83
  RECTAL MUCINOUS ADENOCARCINOMA                3                 10
[1] 2 2
[1] FALSE
D76V9, binary
                    cls
clus                  0  1
  21Q LOSS MUTATED    3 63
  21Q LOSS WILD-TYPE  3 93
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  21Q LOSS MUTATED      3   63
  21Q LOSS WILD-TYPE    3   93
     clus
vv    21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  NO                 3                  3
  YES               63                 93
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  21Q LOSS MUTATED   51  0  4  0
  21Q LOSS WILD-TYPE 70  2  8  3
D76V10, multiclass
    clus
vv   21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  R0               51                 70
  R1                0                  2
  R2                4                  8
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D76V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  21Q LOSS MUTATED       0                         0    35
  21Q LOSS WILD-TYPE     1                         3    46
D76V12, multiclass
                           clus
vv                          21Q LOSS MUTATED 21Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                0                  3
  WHITE                                   35                 46
[1] 3 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 = 22Q LOSS MUTATION ANALYSIS
D77V1, survival
                    sevent
clus2                 0  1
  22Q LOSS MUTATED   40  8
  22Q LOSS WILD-TYPE 88 14
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                48                102 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
                 8                 14 
$`22Q LOSS MUTATED`
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       13.55        14.50        15.39        10.39        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 
        7.07         2.01        34.03        29.98         1.02        19.99 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02         1.02        19.99        28.04        36.03        14.04 
TCGA-AG-A00H TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6544 
       25.97        12.00        10.98         1.94        38.96         0.49 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 
        0.72        10.19         6.05         4.73        13.97        10.98 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97         7.10        30.05        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DG TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6512 TCGA-EI-6881 
       41.36        51.48         2.40        20.55        17.69        16.41 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
       14.86         0.39         0.66         0.76        18.28        26.43 

$`22Q LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3580 
       37.74        10.39         8.45        20.02        36.03         8.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        1.02        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 
        7.99         0.99        32.98         0.99         0.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       31.00        70.03        64.01        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04         1.45         0.69         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.97         9.37        60.03         7.99        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        36.00        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        57.24       129.27        24.13        32.61         0.49 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       11.97         8.45         9.96        37.51        31.30         1.02 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.46        55.76        47.08 

  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
              0.39               0.46 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             51.48             129.27 
  22Q LOSS MUTATED 22Q LOSS WILD-TYPE 
             13.30              15.95 
[1] "0.4 - 51.5 (13.3)"  "0.5 - 129.3 (15.9)"
[1] "hr=" "2.2"
D77V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  22Q LOSS MUTATED         7        2        14         0         1         3
  22Q LOSS WILD-TYPE      23        6        24         2         1         2
                    vv
clus                 STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  22Q LOSS MUTATED            4         12          2        7         3
  22Q LOSS WILD-TYPE          5         11         12       11         6
D77V3, multiclass
            clus
vv           22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  STAGE I                   7                 23
  STAGE II                  2                  6
  STAGE IIA                14                 24
  STAGE IIB                 0                  2
  STAGE IIC                 1                  1
  STAGE III                 3                  2
  STAGE IIIA                4                  5
  STAGE IIIB               12                 11
  STAGE IIIC                2                 12
  STAGE IV                  7                 11
  STAGE IVA                 3                  6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 T1 T2 T3 T4
  22Q LOSS MUTATED    1  9 42  5
  22Q LOSS WILD-TYPE  8 20 67  9
D77V4, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  T1                1                  8
  T2                9                 20
  T3               42                 67
  T4                5                  9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 N0 N1 N2
  22Q LOSS MUTATED   23 24  9
  22Q LOSS WILD-TYPE 60 21 23
D77V5, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  N0               23                 60
  N1               24                 21
  N2                9                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                    vv
clus                 M0 M1 M1A MX
  22Q LOSS MUTATED   41  9   0  6
  22Q LOSS WILD-TYPE 82 13   2  7
D77V6, multiclass
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  M0                41                 82
  M1                 9                 13
  M1A                0                  2
  MX                 6                  7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V7, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   25 32
  22Q LOSS WILD-TYPE 49 56
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     25   32
  22Q LOSS WILD-TYPE   49   56
        clus
vv       22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  FEMALE               25                 49
  MALE                 32                 56
[1] 2 2
[1] FALSE
D77V8, binary
                    cls
clus                  0  1
  22Q LOSS MUTATED   51  4
  22Q LOSS WILD-TYPE 92  9
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED     51    4
  22Q LOSS WILD-TYPE   92    9
                                clus
vv                               22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                        51                 92
  RECTAL MUCINOUS ADENOCARCINOMA                4                  9
[1] 2 2
[1] FALSE
D77V9, binary
                    cls
clus                   0   1
  22Q LOSS MUTATED     3  54
  22Q LOSS WILD-TYPE   3 102
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  22Q LOSS MUTATED      3   54
  22Q LOSS WILD-TYPE    3  102
     clus
vv    22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  NO                 3                  3
  YES               54                102
[1] 2 2
[1] FALSE
                    vv
clus                 R0 R1 R2 RX
  22Q LOSS MUTATED   41  1  5  0
  22Q LOSS WILD-TYPE 80  1  7  3
D77V10, multiclass
    clus
vv   22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  R0               41                 80
  R1                1                  1
  R2                5                  7
  RX                0                  3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D77V11, continuous
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  22Q LOSS MUTATED       0                         1    28
  22Q LOSS WILD-TYPE     1                         2    53
D77V12, multiclass
                           clus
vv                          22Q LOSS MUTATED 22Q LOSS WILD-TYPE
  ASIAN                                    0                  1
  BLACK OR AFRICAN AMERICAN                1                  2
  WHITE                                   28                 53
[1] 3 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 = XQ LOSS MUTATION ANALYSIS
D78V1, survival
                   sevent
clus2                 0   1
  XQ LOSS MUTATED    19   2
  XQ LOSS WILD-TYPE 109  20
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
               21               129 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
                2                20 
$`XQ LOSS MUTATED`
TCGA-AF-2693 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3600 
       19.10        12.00        32.02        24.00        34.03         6.05 
TCGA-AG-3732 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A02X 
       32.98        13.94        23.01        31.00        64.01        41.00 
TCGA-AH-6544 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DE 
        0.49        10.19        13.97        30.05         5.29       129.27 
TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6571 
       32.61        11.97        31.30 

$`XQ LOSS WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       10.39        36.03         8.02         7.07         1.02         2.01 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 
       17.03         0.99        20.98         6.02        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       15.95        36.03         9.07         1.02        12.00        70.03 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.04         1.45         0.69         0.72         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
       12.00        15.02        36.00         7.10        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06       126.44        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
             0.49              0.39 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
           129.27            126.44 
  XQ LOSS MUTATED XQ LOSS WILD-TYPE 
            24.00             13.97 
[1] "0.5 - 129.3 (24.0)" "0.4 - 126.4 (14.0)"
[1] "hr=" "2.3"
D78V2, continuous
                   vv
clus                STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC STAGE III
  XQ LOSS MUTATED         5        3         7         0         0         0
  XQ LOSS WILD-TYPE      25        5        31         2         2         5
                   vv
clus                STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV STAGE IVA
  XQ LOSS MUTATED            2          1          2        4         0
  XQ LOSS WILD-TYPE          7         22         12       14         9
D78V3, multiclass
            clus
vv           XQ LOSS MUTATED XQ LOSS WILD-TYPE
  STAGE I                  5                25
  STAGE II                 3                 5
  STAGE IIA                7                31
  STAGE IIB                0                 2
  STAGE IIC                0                 2
  STAGE III                0                 5
  STAGE IIIA               2                 7
  STAGE IIIB               1                22
  STAGE IIIC               2                12
  STAGE IV                 4                14
  STAGE IVA                0                 9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                T1 T2 T3 T4
  XQ LOSS MUTATED    0  8 17  0
  XQ LOSS WILD-TYPE  9 21 92 14
D78V4, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  T1               0                 9
  T2               8                21
  T3              17                92
  T4               0                14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                N0 N1 N2
  XQ LOSS MUTATED   16  4  5
  XQ LOSS WILD-TYPE 67 41 27
D78V5, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  N0              16                67
  N1               4                41
  N2               5                27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                   vv
clus                 M0  M1 M1A  MX
  XQ LOSS MUTATED    18   5   0   1
  XQ LOSS WILD-TYPE 105  17   2  12
D78V6, multiclass
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  M0               18               105
  M1                5                17
  M1A               0                 2
  MX                1                12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V7, binary
                   cls
clus                 0  1
  XQ LOSS MUTATED   14 11
  XQ LOSS WILD-TYPE 60 77
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     14   11
  XQ LOSS WILD-TYPE   60   77
        clus
vv       XQ LOSS MUTATED XQ LOSS WILD-TYPE
  FEMALE              14                60
  MALE                11                77
[1] 2 2
[1] FALSE
D78V8, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED    21   3
  XQ LOSS WILD-TYPE 122  10
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED     21    3
  XQ LOSS WILD-TYPE  122   10
                                clus
vv                               XQ LOSS MUTATED XQ LOSS WILD-TYPE
  RECTAL ADENOCARCINOMA                       21               122
  RECTAL MUCINOUS ADENOCARCINOMA               3                10
[1] 2 2
[1] FALSE
D78V9, binary
                   cls
clus                  0   1
  XQ LOSS MUTATED     1  24
  XQ LOSS WILD-TYPE   5 132
[1] "tbl2"
                   cls
clus                [,1] [,2]
  XQ LOSS MUTATED      1   24
  XQ LOSS WILD-TYPE    5  132
     clus
vv    XQ LOSS MUTATED XQ LOSS WILD-TYPE
  NO                1                 5
  YES              24               132
[1] 2 2
[1] FALSE
                   vv
clus                 R0  R1  R2  RX
  XQ LOSS MUTATED    17   0   3   1
  XQ LOSS WILD-TYPE 104   2   9   2
D78V10, multiclass
    clus
vv   XQ LOSS MUTATED XQ LOSS WILD-TYPE
  R0              17               104
  R1               0                 2
  R2               3                 9
  RX               1                 2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D78V11, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  XQ LOSS MUTATED       1                         0     9
  XQ LOSS WILD-TYPE     0                         3    72
D78V12, multiclass
                           clus
vv                          XQ LOSS MUTATED XQ LOSS WILD-TYPE
  ASIAN                                   1                 0
  BLACK OR AFRICAN AMERICAN               0                 3
  WHITE                                   9                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"
